Yu-Gi-Oh!/WMG

Joey and Mai are somehow closely related.
Mai likes purple so much that she wears purple novelty contact lenses. Consider the Hot Bloodedness, the charm, the lightly wavy blonde hair, the purple outfit Joey sported in Season Zero, etc.

Between Yu-Gi-Oh! Season Zero and Yu-Gi-Oh! Duel Monsters, Seto, perhaps while his mind was broken after Yami Yugi broke it in the first episode of Duel Monsters, gave money to Joey.
If you've seen/read both Season Zero and Duel Monsters and pay close attention, you'll notice that in Season Zero Joey worked multiple jobs to pay off his alcoholic dad's gambling debts, and in Duel Monsters he has the free time for spending weeks playing card games on islands/blimps/etc., hang out with Yugi after school often lounging around, and otherwise wasting his youth away, no sign that Joey's poor, as abused, or working.
 * You bring up a valid point regarding Jounouchi's economic status (although he's not rich either or else he'd be able to afford his sister's operation without the Duelist Kingdom prize money). But I kind of doubt Kaiba would just suddenly give Jounouchi any sort of present, let alone a ton of money. Broken mind or not, that just seems too OOC for Kaiba (besides the 'broken mind' was more like a full-blown coma that lasted for several months in the manga, I doubt Kaiba would be giving anything to ''anyone' in that state). SOMEthing must have happened to at least put Jounouchi into a stable economic position, a position where he's also able to afford maintaining a deck for a trading card game which is supposed to be a bit pricey if you go by some real life TCGs. The real question is, if it wasn't Kaiba then what could have caused it?
 * Maybe Mokuba gave Jounouchi money.
 * Or maybe Jounouchi started gambling and won money that way.

Yami Yugi inspired Kaiba to create holographic Duel monsters.
In the tenth chapter of the original manga, when Seto Kaiba introduced the card game to Yami Yugi, Yami Yugi making Kaiba go into a dream state where the monsters turned and attacked Kaiba, it was the first instance of real monsters, and the green-haired brat was completely taken by surprise. Next we know, Seto Kaiba is selling holographic field-things and a bit later duel disks. Duel Monsters may have been his game, but according to the manga Yami Yugi was first to show the concept of bringing the monsters "alive."
 * In the english version of the manga, when Kaiba first shows off his holographic dueling system by using it against Yugi's grandpa, Kaiba actually says (or thinks, can't recall which and I don't have the manga in front of me right this moment) "I've recreated my duel with Yugi using virtual reality! My money can buy powers just like his!"
 * But that brings up a bigger question. In the english manga, when Kaiba is explaining to Yugi's grandpa how his holograms work, a very tiny speech bubble adds that the holograms are processed using a microchip in the cards. So how did Pegasus know enough of the future to realize he'd need to put microchips in all the Duel Monsters' cards?? I thought the Millennium Eye was supposed to read minds/see into the heart of someone else and the Millennium Tauk was supposed to see through time, not vice virsa.
 * Pegasus did meet Isis, but he met her when he needed to seal the power of the Egyptian God cards he couldn't control. Which was not until after he'd started making his card game. So it doesn't seem likely that she could have given him a heads-up about the whole microchips and holograms thing....
 * Maybe Pegasus was just Crazy Prepared. He is supposed to be a painter after all, perhaps his inner artistic genius decided that his card game needed microchips in case of some future development.

Atem suffered from cabin fever.
Word of God pretty much establishes that when Yugi first managed to get Atem's spirit out of that puzzle, Atem was a total evil psycho. Some people say because he's all darkness separated from his "light" half. Personally? I say who WOULDN'T have gone stark raving mad if they found themselves in the same situation? Just think about it for a moment: Atem seals himself inside an enchanted metal puzzle after stripping himself of memories of his own identity. Word of God said he was aware of time passing as he was stuck inside the puzzle. He spends approximately the next 3000 years inside the puzzle waiting for someone to take it out of a dark tomb in the middle of a desert. Atem spends all this time supposedly in isolation, and he couldn't even DO anything. It's not like he could take a walk around the tomb if he got bored or play solitaire or a video game or anything. If 3000 years isn't enough to cause someone to go stir-crazy then I don't know what is. All this seems to point to Atem having one of the worst cases of cabin fever in human history.
 * Seconded: And I Must Scream - Effect

The best duelists are those who have or who in a past life had a Millennium item.
It will always be this way, with the incarnations of Yugi and co being the best. Reasons include: The Millenium items channel power into the honest owner's cards. Those who own Millennium items and/or have increased connections to said power are most worthy of having better duel monsters serve who they're faithful to, a.k.a. royalty a.k.a. the mill item wielding duelist. Willingness on the monsters parts have been shown to correlate with likelihood of winning duels.
 * This theory explains how the heart of the cards come through for Yugi, a former pharaoh in a past life, over other characters who also believe in the heart of the cards
 * Seto has some kinda unusual bond with his Kisara/BEWD, Marik believes in the power of the god cards though perhaps takes it for granted, everybody refers to their monsters as if they were sentient, etc.
 * I think a modification might be "has a connection to the supernatural at the level of the soul". Past lives that had magical power are usually the best way to have such a connection, and Millennium Items are the most common way for it to develop, but being a reincarnation of the Supreme King of all Duel Monsters or being the can for 1/5 of a dragon god work just as well, the former due to continuation of old loyalties combined with present trust working just as well as a human kingship like Atem's, and the latter because of the combination of trust and monsters being loyal to the human as the dragon's proxy.

Tristan duels himself in his pervy trenchcoats
during( some of) the duels and/or otherwise when nobody's paying him attention. This explains why he mellowed( and started wearing the trenchcoats) after Toei Animation's Season Zero. Tristan isn't as much a card-game nerd as his peers, yet there he is watching his friends throw cards at each other during his spare time every day, out of his obligation to always be there when his support is needed. This is kinda stupid, but I still wanted to share.

Miho (from Season Zero) was killed by a yo-yo.
This memetic clip of Honda(Tristan)'s daydreaming was foreshadowing Miho's fate. Yo-yos are the only evil that wasn't defeated and Honda is pretty sharp when it comes to minor details and those he loves so he possibly unconsciously saw it coming.
 * Honda became the quiet guy we better know as a result of his heart having been broken from Miho's tragic death by the yo-yo.
 * Officially jossed by GX of all things. She was briefly seen on Trueman's list, along with several other opponents Atem defeated during the first series.

Seto Kaiba is a half-Vulcan.
Kaiba doesn't age between Yu-Gi-Oh! Duel Monsters and Yu-Gi-Oh! GX, even though a decade had supposedly passed. Kaiba seems the most logic-oriented and level-headed most of the time. He has that outdated ugly haircut (that had not been dyed a human color yet and was still green back in Season Zero) and (nerdishly pale) alabaster green skin. His Tsundere-personality seems to switch between emotionless, logic-oriented, narrow-minded, to struggling with his identity as a being of emotion. His unpointed ears are simply from his human genes. His BEWD jet is a spaceship. His fighting moves are never explained, especially considering he's a nerd. His inventions could be the products of a combination of his own alien technological advancements and those of his step-father. His parents died upon landing on Earth. The name Seto sounds a lot like SETI, which is the acronym for 'Search For Extraterrestrial Intelligence.' He dresses like an alien, with that bulleted tinfoil trenchcoat and those OOC S&M-esque buckles about his arms; and the way 4Kids dubbed guns means when he holds a gun it looks like he's holding a loaded finger, which isn't human.
 * Puppyshippers would get along with K/S-shippers.
 * As a Spock/Bones and Kai/Jou shipper, I disagree. Joey is much more The McCoy than The Kirk anyway, even though he is take-charge.
 * I recently took up rewatching Star Trek and agree completely.

== During Marik's tombkeeper's initiation, which was traumatic enough to complete the separation of Marik and his hatred, Marik's father didn't just carve magical hieroglyphics into Marik's back while everybody watched; Marik's father also raped Marik ==  after carving the hieroglyphics, though the rape was off-camera due to Marik being blinded by the similar pain in his back so we don't witness it. (Rape and inbreeding wouldn't be unheard of in an ancient underground cult like those tombkeepers, don't ya think?) Marik( and us viewers) don't see( and thus KNOW that) Marik was raped, though Marik was still effected and made to wonder what events took place specifically. This is where Yami no Marik got his powerful fetish for raping the minds of random people and killing them.
 * Look, enough with the rape already. Sheesh. Is having hyeroglyphs carved into your back with a burning knife not horrifying/evil enough for you, you need to include rape just to spice it up? (As a sidenote, from a legal standpoint, the former is regarded as slightly more serious than the later, just to put things into perspective.)

Part of the rules of Duel Monsters in this universe is that no one has to shuffle before a game.
As discussed in The Magic Poker Equation, everyone seems to come up with the exact monster or spell they need that allows them to win the match when they need it. Furthermore, every character seems to rely on one special monster. (Yugi always seems to draw Dark Magician; Seto always seems to draw Blue Eyes White Dragon; etc.) There are only two ways this is possible, and one (a small deck) is visibly false. Therefore, there can be nothing in the rules that says you can't stack your deck, and so everyone does.
 * There are a couple of shuffling incidents in the anime. Before Yugi duels Pegasus, Yugi makes a point of shuffling Pegasus's deck. Pegasus chooses not to shuffle Yugi's, though. And one of Yugi's opponents in the Battle City arc pulls a stacked deck cheat, which Yugi anticipates and foils.
 * If the WMG is true, then the stacked deck isn't a cheat -- it's a strategy.
 * By the time of 5Ds, this becomes a moot point. The Duel Disks clearly have an auto-shuffling system. Depending on how those work, that could mean the decks are stacked whether the players know it or not.

Duel Monsters are made of People!
The Memory World arc showed that each person has a Duel Monster within them they can summon; it's called a ka. Not surprisingly, ka is the Egyptian term for the personality or heart of a person, one half to a person's "soul"; the other half is their life energy, or ba. Also, in a duel, one can use their ba (life energy) to strengthen their ka Duel Monster (and other Duel Monsters they summon), and these creatures literally live inside a person. To gain strong monsters for the coming war, Akhenaden and the other priests are shown ripping people's ka from their bodies and sealing them in tablets. Thus, the Shadow Realm's English meaning of death is apt; when a person dies in the YGO universe, their soul becomes the Duel Monster their ka represents. It also explains why no one refuses to duel, even if dueling means ludicrously high stakes, and why dueling is such an obsession in the universe: their soul's nature as a Duel Monster compels them to duel, no matter what.
 * It certainly holds with the true identity of the Blue Eyes White Dragon. But does this theory allow for still-living people to secretly be duel monsters? Yugi does seem to have an affinity for Kuriboh...
 * GX revealed that Duel Spirits are extradimensional aliens. It would appear that Egypt was the first Earthly civilization to have contact with there creatures, thus inspiring their concept of ka and ba. Cool, huh?
 * Ba and Ka aren't ideas; they're truths, as shown by the Ancient Egypt arc and the transition from Mahado to Dark Magician. As such, it must be concluded that the other dimensions seen in GX, rather than being simple parallel universes inhabited by monstrous beings, are the afterlife, one possibly worse than Soul Society.
 * Hmm, that Ka thing sounds a lot like Summoning a Persona.

Yu-Gi-Oh takes place in the Stargate Verse several years after the end of the series.
It thus follows that: A possible alternative: if one goes by the dub date of "five thousand years," that puts Atem's rein almost exactly at the time of Earth's rebellion and the expulsion of Ra. Stargate Verse never did explain how humanity pulled that off... and why Ra didn't make the trip, several centuries of travel or no, to reclaim the planet, wipe out a bad precedent, and avenge his humiliation.
 * The Millennium Items are Goa'uld technology. It makes sense. They're mysterious artifacts which seem to have magical or godlike properties. The eye appearing on them looks an awful lot like Ra's symbol; perhaps he built them to further the illusion of godliness.
 * Yami Yugi, Yami Marik and Yami Bakura are all symbiotes. They can take over their hosts' bodies at will, they speak in different voices when in control, they're smart, etcetera. The difference is that Yami Marik and Yami Bakura are both Goa'uld, whereas Yami Yugi is a Tok'ra.
 * KaibaCorp's hologram technology is alien in origin. He bought it from the rogue NID. He has money, after all. He can screw the rules.
 * This theory goes well with the above allusions to an ancient alien civilization that came to Egypt in the past. So the Millennium Items are some kind of stasis jars for the symbiotes, as well as powerful items. The Eye builds on mind-reading technology, of course. But what are the monsters themselves? Some kind of Ancient technology we've never heard of before?
 * The monsters could be documentation of various aliens encountered by the Goa'uld; the card stats reflect facts about these creatures.

The Blue-Eyes White Dragon was Kisara's daemon.
An animal spirit representing her soul, separation from which will cause her death. After that happened, she gave it to her lover, thus...

The Blue-Eyes White Dragon (and by extension, Kisara herself) is Kaiba's daemon.
Hence his obsession with owning them all and their empathy.
 * Clearly, she gave her life via daemon transplant to save his when he lost his original daemon. (Hey, it can happen -- watch The Golden Compass!)
 * If he wanted her empathy, then he wouldn't be using the Blue Eyes to ruthlessly dominate his opponents, beatdown-style, knowing that no one else would have that relatively easy level of power at hand, often taunting them, especially when they have weak cards. Kisara should be spinning in her grave.
 * What do you expect? Especially before his "soulsplosion," Kaiba's an asshole. He does get better over the course of the series.

Kaiba had Pegasus create the Kaibaman card as a way for him to be with Kisara.
After being hinted in the Doma Arc, it's confirmed in GX that the spirits of real Duel Monsters all exist in a parallel world. The Blue-Eyes White Dragon's spirit would have to be Kisara. Now that Kaiba's created a card version of himself, its spirit will exist in the same world.
 * Kaibaman is an avatar.

Rex Raptor is L.
They're both called Ryuzaki. End of story.

The world of Yu-Gi-Oh is actually a rational universe, and it only appears insane because we're viewing it from our universe
Each one is marked by an obsession and complete domination by something - for them, card games, for us, the internet. Which is more likely to dominate the globe, card games or Lolcats?

Rex Raptor is an alternate L.
In a universe without Duel Monsters cards, Ryuzaki became a famous pop star once he finished puberty and lost the Dub Voice. Death Note takes place years after Yu-Gi-Oh, and so L took his name from the now well-known singer Ryuzaki.
 * Seto Kaiba looks too much like Light Yagami not to be him...
 * Not just looks. If Kaiba could lie or keep a straight face, then he and Light would be exactly the same person. There is evidence in the first volume of the Death Note manga. Seriously.

Joey is related to Wheeler in Captain Planet.
He has the same name and accent, and his favorite card is fire-themed. They were separated at birth... in America!

Joey's dad is Wheeler.
That would mean that Wheeler grew up to be a dirt-poor, dangerous, alcoholic asshole who lives in a hovel in the slums and beats his son. Yaaaaay.
 * Time frame sort of fits. He knocked up Linka when they were teens.


 * Well, Jounochis father grew up to be a violent alcoholic. Joeys father might actually be Wheeler from Captain Planet who leads a normal life and loves his son (even though he still got divorced)
 * This means that there's an alternate universe where Captain Planet was a Darker and Edgier anime.

The Shadow Realm is a Fate Worse Than Death
Think about it. In the original, people just died. In the dub, their memories, minds, and even their souls are sent to this unseen dimension which may be filled with various tormenting images or visions without end. It's "Go directly to hell; do not pass Go, do not collect 200 cards."

The Shadow Realm is Silent Hill
See above. The cards are a focusing method allowing people to concentrate and weaponise their emotions, desires and fears and bend them to their will. With defences down, a person's survival comes down to the emotions of their victorious opponent, killing them or stripping them of their soul, fitting the hints at what befalls people who can't escape Silent Hill. The transport is always initiated by the spreading of a creepy, vision obscuring fog.

Both games are made by Konami.

The cases of completely ignoring the game's rules is an example of the town's typical abandoning logic just to torment its victims.

Yugi and Solomon Muto are the same person - that is, Yugi is his own grandfather.
Consider the following: Yugi is abnormally short. Grandpa is abnormally short. Yugi has an eccentric hairstyle, composed of a small bit of styled fringe in the front and a bunch of spikes in the back. Grandpa has an eccentric hairstyle, composed of a small bit of similarly-styled fringe in the front and a bunch of spikes in the back (held down by his bandana). Yugi has purple eyes, an odd color. Grandpa has purple eyes, an odd color. Yugi is a gaming expert who has almost never lost a duel. Grandpa is a gaming expert who has almost never lost a duel. Yugi learns a lot about the Millennium Puzzle and Egyptian myths through his interaction with Yami. Grandpa knows a lot about the Puzzle and Egyptian myths before the story so he can Info Dump. With all of this information, combined with the bizarre sorts of mystical things that happen in Yu-Gi-Oh!, it isn't hard to imagine a Stable Time Loop causing Yugi to go back in time, call himself Solomon (perhaps to hide his real identity), and become his own grandfather.

Kazuki Takahashi wrote this manga because he's psychotic
Think about it. In the original run (vol. 1 - 7), people are constantly being killed without Yami, Honda, Jonouchi or the nine-year-olds who worship Kaiba batting an eye. The Duelist Kingdom arc was written while Takahashi was on medication and intensive therapy; hence, the focus on a much less violent subject. His occasional outbursts of medication failure are shown with the Player Killer of Darkness (aka Panik) and Bakura pulling out Pegasus' millenium eye and licking. During the Battle City arc, he stopped taking his medication. Thus Marik. Unfortunately for the rest of us, he began self-medicating during the Millenium World arc (the occasional outbursts of violence, but less than the original).
 * Ha, interesting theory. Although ironically, the only time he was heavily medicated was during the Millenium World arc, hence Zorc's rather...unconventional design.

A challenge to duel in the presence of a millenium item is automatically turned into a Compulsion spell.
Think about it: One theory is that if you forgo a duel, including the Shadow Games pre-Duel Monsters, then you automatically get sent to the Shadow Realm. Why would people, sometimes not Too Dumb to Live or too proud to back down, accept a challenge from someone who looks like a high school kid with funny hair (or a middle school kid, in most of the first series)?

If they knew they would be sent to the Shadow Realm for refusing, they would be a heck of a lot more scared.

On the few occasions that they know the risks ahead of time and have nothing to win (nitroglyceryn hockey springs to mind, although he was an idiot), they still accept the challenge. In the earlier episodes, such as when Yugi is playing the "take what money you can stab off your hand" game, it is shown that the items can enhance or even alter people's actions during a Shadow Duel; why not before?

Yugi is crazy!
Yugi snapped and developed a duel dual duel personality. His friends felt bad because no amount of therapy would help him. They all decided to play along with his delusions of Magic and Monsters. Tea plays his love interest, Joey the best friend, and Tristan is just the observer who might as well be a background character. Kaiba is also Yugi's friend, and he also plays along; he has so much money that he hires actors to sustain the charade. He was friends with Pegasus, who is a bit of a goof ball and who agreed to play along as well. Bakura is the same, but he tends to get into it. Even the part with Noah was faked, but Noah may be related to Seto anyway. It's all an elaborate game. Later, Seto builds a school for people with similar delusions.....
 * Shutter Island, anyone?  Here we go.
 * I love the "And later Seto builds a school for people with similar delusions". Duel Academy Island IS Shutter Island!

Joey is the most skilled duelist on the show by far.
Based on the The Magic Poker Equation. Joey is, and in his world is known to be, one of the luckiest duelists in the world, perhaps luckier than even Kaiba and Yugi - who seem to manipulate fate to get the desired cards. The magic poker equation is: luck = skill * importance. Joey's latter value, importance, is nowhere near as high as Yugi's. While Joey's life is threatened more than once, the fate of the entire world has never rested on his shoulders. So, seeing that Yugi's duels' importance > Joey's duels' importance (their personal importance is also Yugi > Joey for obvious reasons), since Yugi's luck ≈< Joey's luck, then Joey's skill > Yugi's skill.

That ignores that Yugi's (and possibly Kaiba's) luck is a result of l=sid (luck = skill * importance * desire). Both Yugi and Kaiba have high values of desire. If desire isn't in Joey's equation, that requires him to be even more skillful for Joey's luck >= Yugi's luck.


 * This all ignores one important, oft-overlooked factor: Joey has a lot of useless draws/hands. Ergo, the Magic Poker Equation still holds.


 * It's obvious! Joey's a probabilopath!


 * I thought this theory was pretty much confirmed... oh, you know, the time he ALMOST BEAT MARIK?

Yami Bakura is the best duelist.
In his first duel with Yugi, he didn't topdeck and he almost won; he lost because his own duel monster was normal Bakura, who betrayed him. Then he would've won his next, but Yugi went all Egyptian God on him; then...you get the point. Bakura is better than Joey is better than Marik is better than Kaiba is better than Yugi is better than a dead fish.


 * You could also say that Yami Bakura lucked out by already having Dark Necrofear, Dark Sanctuary, and Ouija/Destiny Board cards ready for his big strategy beforehand. And besides, Yugi is the best duelist on the show.
 * First duel, though, in episode 13. He didn't even play a monster with more than 1k attack points. And it's implied that Dark Sanctuary is automatic when Dark Necrofear dies. As for Yugi being the best, it's implied he lost a duel to Joey. So Joey > Yugi.
 * Nothing is implied, other than Joey getting his Red Eyes back. Yugi could have just decided to give it back for a great duel, and Joey decided to finally accept it.
 * Yugi is the best duelist because the plot requires it.
 * I disagree; his Ceremonial Duel was far and away the best display of dueling prowess of any duelist in any of the series.
 * One other thing, Yami Bakura came close to winning during the Millennium Arc only because of the most broken mill strategy on the planet.

In a realistic universe, Yugi wouldn't be the master of cardgames.
He would be a good player, but not the best. He could never beat Kaiba at Chess because you can't win a game of chess by coincidentally having a good piece. If one of the players knows about strategies, then you're smashed.
 * That's probably why we never saw them play chess, but only the watered down version, Capsule Monsters, against Mokuba. Yugi would have lost. Unless it would have been some kind of shadow game in which the other chess pieces' spirits protect the king, but that would have been too ridiculous, even for Yu-Gi-Oh.

Also, Yugi wins mostly because he believes in the heart of the cards. In the first volumes of the manga, the reasons for his winning were credible. Intuition, logical thinking, etc. But it's hard to stay logical once ancient Egyptian pharaohs enter the picture.

Also, Yami Bakura would have won.
 * Ahem. I could counter these two by saying that Kaiba himself wouldn't be able to rely on an arsenal of beatdown pieces, which make many of his duels somewhat one-sided. (And which is the chief reason, pure Seto/Kisara-shippers be damned, that he relies on the Blue Eyes White Dragon.) And if you're talking strategy, it takes a lot more to rely on weaker cards, which he did in his ceremonial duel, on top of actually thinking several steps ahead in his moves. Not to mention that "heart of the cards is mostly 4Kids' doing.
 * I agree with most of your points, but Kaiba is incredibly proficient at strategy games. He beat one of the best chess players in the world at age 10 (12 in the Dub).


 * During Battle City, where he topdecks Osiris/Slifer, I'll give you, but during the Millennium Arc, Yami Bakura relied on the most broken mill deck in the history of the game, and one that shouldn't even exist. And Yugi still proved his ability to think ahead by having just the right monster removed from play until the next turn, ready to deliver the final blow.
 * Furthermore, Yugi still would have won in Battle City because Bakura first topdecks Jowgen the Spiritualist, a card that's completely out of place in his deck and there's no reason he would have.

In addition, Mai would be a great duelist. She couldn't beat Marik because she couldn't read the text? That's definitely a plot device. If they had been playing on the table, the way we do in Real Life, then she definitely would have won.
 * Yes, but remember in Real Life you can't use Harpie Lady Sisters as the only tribute for Ra or use Amazoness Chainmaster to take a card directly from your foe's deck.

Yu Gi Oh: The Abridged Series is the actual show; the "real" show is just a bad fanfic!
This would explain a great number of things, including why tropers routinely cite The Abridged Series instead of the "real" show in the example listings.

Atem allowed Mana to use him as a dress-up doll
There are probably other reasons why he's wearing enough gold accessories to destabilize a small country's economy, but none that are cuter.
 * He's a pharaoh. We may not know how pharaohs dressed day-to-day, but have you ever seen the stuff Tut was buried with? The gilding on Tut's coffin? Its practically the uniform of the job.
 * Then again, Tut also had a girl of a similar age he was close to. Coincidence? Yes. Or is it?
 * I've just been doing a little bit of reading on their culture and it seems Ancient Egyptians all but invented bling, so it doesn't strike me as unusual. What I want to know is how he gets the ones on his legs to have such a tight fit without cutting off the circulation.

Gearfried The Iron Knight is based off an EVA.
Human souls inside a suit of armor that are more fearsome when their armor falls off. Haven't heard that one before.
 * They look alike, so they could be alike.

A lot of people are going to be in for a big surprise when they get to the afterlife.
We have undeniable proof that the Egyptian afterlife is real. We haven't seen any other indisputable afterlifes. Occam's razor says that the Egyptian afterlife is the only true one, while all the other ones are fictitious.

Most people have probably neglected getting their funeral items and burial rituals prepped...

If the Egyptian Afterlife is the only real one, then we also have the Ba Charge issue: that is, Egyptians mummified their corpses on the premise that the conscious-spirit ka would survive only so long as the animal-energy-spirit ba could recharge it through the body. Destroying a mummy killed the soul of the dead person in the Land of Sunset. Because Atem's tomb collapsed, he might have spent about a day in the afterlife before going out like a candle. Go, Yugi.
 * That would be a very thinly populated afterlife.
 * Atem could rely on Yugi's body for charge. But if he comes back and visits Yugi every night the way his religion stipulates, then it makes the ending kind of a joke and wrecks the bildungsroman. And it puts a weird spin on GX, which is already weird.
 * In either case, Yugi needs to locate a good embalmer.
 * Y'all forget one thing - in the Yu-Gi-Oh! version of the Egyptian afterlife, people can fuse their ba with their ka to gain immortality at the cost of humanity (see- Dark Magician/Mahad, Dark Magician Girl/Mana, BEWD/Kisara). Presumably, when bodies are destroyed, the ba leaves to to join with the ka, monsterifying the person. "Yami" probably simply had a short human afterlife.
 * Does that mean he turned into a Yamask?
 * Dan Green apparently voiced Yamask (according to Bulbapedia). Make of that what you will.

The alternate dimensions in GX are populated by monsters formed by people who weren't mummified.
Now, those afterlives are crowded...

There are three Mariks.
There's the Marik we see for most of the Battle City arc, who has the nasally voice; there's the Marik who has the stretchy face and popped-out veins; and there's the one who talks like "Namu" and only appeared after Battle City was over. Basic Marik and Namu-voice Marik have almost the same memories, but Namu-voice Marik didn't get to choose to do stuff; he only had the memories of having done the evil stuff, if that makes sense. He still feels guilty for his body and part of his soul (the Basic Marik part, since we don't know whether Dark Marik shares in the Marik soul) doing the evil stuff; but since he didn't do it himself, but only remembers doing it from a first-person perspective, he gets let off the hook. So he's less a Karma Houdini than he might appear at first glance.

Namu-Voice-Marik did seem to have a completely different personality from Basic Marik, even more different than Basic Marik is from Dark Marik; but he didn't seem "fake" or flat like "Namu" did.

Marik (and Yami Marik, for that matter) is incompetent.
The only times we see or hear about Marik dueling, he duels like an idiot:
 * Yami Marik mentions that Isis / Ishizu could beat him / Normal!Marik with ease. Not that Isis is a bad duelist, but it doesn't do much to suggest that Marik is a competent duelist if he consistently stood no chance against his own sister.
 * When he was ten. A lot has changed since then.
 * Which brings up another point: how the hell did they get trading cards underground with no contact from the outside world? And that's ignoring the fact that the card game would've not been created yet or just started six years before the events of the series.
 * When dueling through Jounouchi, Marik wanted Jounouchi to take Red Eyes from Yugi via Exchange. It would've stopped Yugi from using it, but Marik wouldn't have been able to summon Red Eyes because he didn't have the sacrifices for it.
 * His objective was to take the card so a) Yugi couldn't summon it and b) couldn't use it to get through to Joey. It makes sense from that perspective.
 * Yami Marik comes two seconds away from losing to freaking Jounouchi. He would've lost had Jounouchi stayed conscious for long enough to attack with Gearfried.
 * Even before this, Mai would've beaten Yami Marik with his own god card if it wasn't for that ancient Egyptian chant rule. To put that duel in perspective, Yami Marik has the powers of the shadow realm, an ancient Egyptian lineage, his Millennium Rod, and his god card. Mai's only superpower is of the most-common variety. Muggles Do It Better indeed!
 * Marik's entire deck theme revolves around recycling Monster Reborn to revive Ra over and over again... for one turn. And at a cost of 1000LP each go-around. Ra may have a lot of crazy hidden powers, but Marik can actually read the Egyptian card text. He should know full well how Ra works by the time he starts dueling in Battle City.
 * Marik tries to summon Ra with Jam Breeding Machine tokens on at least two separate occasions (once against Mai, once against Yugi). This is actually a terrible way to summon Ra. Had he succeeded, Ra would've towered implacably over his opponent with the unstoppable burning fury of... 1500ATK.
 * At the same time, he outdueled Yugi for most of their match, before Yugi pulled that "send every single card in your deck to the graveyard" card. It's not that Marik's bad at the game, it's that he expects Ra's power and the shadowgame to do the work for him, draining away his opponent's life force. He knows that won't work against Yami so he doesn't try.

Even outside a duel, he's still stupid.
 * "This door is a bitch!"
 * The most jarring example of all is the alliance Normal!Marik makes with Yami Bakura. Yami Yugi may have the excuse of not remembering who / what Yami Bakura actually is, but Marik is a tomb-keeper. His entire life's training is about knowing this kind of stuff. Who did he think the evil spirit of the Millennium Ring was, given that said spirit had an odd fixation with collecting all seven Millennium Items and destroying the Pharaoh?

Duel Monsters had Forbidden / Limited lists from the start.
The one time we see any duelist use Raigeki is the anchor duel between Yugi and Possessed!Jounouchi. That duel was, for all intents and purposes, off the record books. None of Marik's other minions use broken stuff like that (barring the first Rare Hunter's triple-Exodia set) because those duels are all official.
 * Yugi uses Dark Hole in the first virtual world arc. Granted, that story arc probably ran a "traditional" format, either by Kaiba's design or from the Big Five messing up the program.
 * Another duel in which a player uses broken stuff was the first Yami Bakura vs Yami Yugi duel, where Bakura used two Morphing Jars, cards that have been limited in real life since the day of their release. In a situation like this, Bakura probably wouldn't be worried about how "official" his duel was, so long as he won. It's possible that Man-Eater Bug could have also been forbidden, given that...
 * This also explains why the Egyptian God Cards are considered extremely broken. All things considered, the rules for the God Cards in real life aren't all that good. In fact, because they can be killed by a single Man-Eater Bug (see above), it is quite likely that a lot of freebie monster-destroying card effects like Man-Eater Bug and Dark Hole are simply forbidden, if not outright unprinted (or just extremely rare, like Rebecca's Tribute to the Doomed). With cards like that forbidden, taking on a God Card proves far more daunting as you'll have to overpower it to beat it for certain.

The Duel Monsters cards are magical artifacts.
Albeit, modern magical artifacts that nobody knows are magical. Depending on the card, you have greater or lesser quantities of 'magic' within the card. Reacting with the items is what allows people to abuse The Magic Poker Equation, enough cards together (that is, two decks' worth) forms a magical compulsion spell on dueling, and all the super-rare and powerful cards are indestructible. This troper can't exactly remember the scene from season one where Weevil/Insector Haga tossed Yugi's Exodia cards into the ocean but he believes that Joey/Jou managed to fish two out and brought them back not even so much as waterlogged. This nicely solves the Fridge Logic of why things like the God Cards and the Cyberdark Deck were never destroyed - the magic always made them come out of it unscathed. Once Pegasus printed those cards, all efforts to do away with them were doomed to failure.
 * Interestingly, this may have some merit; . If he is to be believed, apparently the Millennium Magic that empowers the cards would've remained dormant and harmless, had the game not been made and brought the magic to the fore in the form of a very accessible medium.

There will one day be a fusion between Blue Eyes White Dragon and Red Eyes Black Dragon
Because they are totally asking for it: similar yet opposite names, exact opposite attribute, and near-identical support (Kaibaman vs. REB Chick, BEUD vs. REBMD, BESD vs. REDD, etc.) Also because a fusion between the two would likely be very powerful.
 * Alternately, it would cancel out the power of each dragon, like a 1-Hit KO version of the Arrow of Light+Polymerization+Zombie monster technique.
 * Purple Eyes Gray Dragon?
 * This Troper is still waiting for Red Eyes Black Magician...
 * BESD is firmly established as being Kisara, but REBD was never given a human identity; for all we know it's from one of the other eleven dimensions filled with Duel Monsters, one of the ones not inhabited by monsterized human souls.
 * This rabid puppyshipper (Kaiba/Jou, for those not in the know) can testify that this is HUGELY popular among this subset of the fandom, to the point where they're almost a Beta Couple. REBD is nearly always given an OC soul and personality. When done right (which it often is), it is freaking adorable. Long story short, if this WMG is confirmed, puppyshippers everywhere will either Squee to death or pull an I Knew It!.
 * Rejoice! It is now confirmed Blue Eyes and Red Eyes can officially fuse together as of Bonds of Time.
 * Sorry, they don't fuse. Paradox does summon the Sin/Malefic forms of both (he even has both of them in play at the same time, as I recall), but he never fuses them or anything like that.
 * I submit to you this: Light and Darkness Dragon

Anzu is the reincarnated form of Mana
My logic may be off here, but... they do look kinda alike, and Anzu has always had a few subtle hints connecting her to the Dark Magician Girl, so why not?
 * Meh. Show me Anzu on a trampoline and I'll consider it.
 * If I find a visual of Anzu on a trampoline, I, and any other person interested, would be much too... distracted to share it.

Ryou Bakura is the most evil person on the show
Think about it- Yami Bakura did all kinds of stuff. He stole, he killed, he licked blood? and where was Ryou in all of this? He was just here. From watching Marik and Yugi, we can see that just because another spirit (or split personality?) took over your body, it doesn't make your own spirit disappear. Which means Ryou must have been there to witness it all and did nothing. Furthermore, he even took credit (for example, in Battle City he claimed he won all the locator cards and got the duel disk). I wouldn't be surprised if he hid behind his innocent face and waited for the right moment to strike! Only he didn't get a chance?
 * No. His conscious is suppressed by Yami Bakura 90% of the time. He isn't the slightest bit aware of what goes on. 5% of the time Yami Bakura poses as him. the other 5% he stands in the background.
 * ...Or that's what he wants you to think.
 * Still no. It's clear that he could easily be unaware of what his dark side is doing with his body, Yugi didn't have a clue that the pharaoh was even around until they met face to face. He even stated that he blacked out with no recollections later on. Hosts are only aware if their alternates let them be aware. The pharaoh and Yugi were equal partners, which is much different, and Marik's case is a little different. Plus Yami Marik is kind of a dick anyway, so he'd let Marik see exactly what he's doing with his body.
 * I kinda agree. While he is unconscious for most of the time, he DOES know that the ring is evil. Have you read the manga, disagreeing troper? The thing stabs him in the chest. And he makes Yami Bakura heavily injure his own hand. And yet he still carries the ring around for most of the time. Even after repeatedly causing harm.
 * However, I do have a different theory on it. I don't think that he's evil, I think that Yami Bakura managed to convince him that he does everything for a greater good.
 * Also, Ryou had definitely an "outsider" position among the group. This was especially harsh in the last story arc of the manga, where everybody gathers around to enter the pharaoh's memories, but Ryou was excluded. Yami Bakura was the only person Bakura had, almost literally, since his family was who knows where. (Fanon (or season 0?) states that they all died in a car crash, which makes Ryou's writing his sister Amane a letter really creepy.) It was also shown at various points that Yami Bakura kind of cared about him, and wanted him to be on his side. Even if it was for selfish reasons, it's possible that Ryou reacted to it. I don't think that it would be wrong to assume that they had some kind of twisted friendship or even relationship (minus the blood and BDSM stuff from the fanfiction).
 * That brings ups a rather interesting point in the manga, where in the Museum the spirit explains that his host built the table top game they are using, not himself, Ryou Bakura. I'm not agreeing he's evil, this could have easily been the spirit messing with Ryou's head, making him believe it was his idea to build the table for his Monster World game or for the Museum (if this is in fact the museum Ryou's father works for, since he's a curator). Or, after regaining his memories, he tricked Bakura into believing he was the victim (his village being destroyed and his people sacrificed in the name of the Pharaoh) and Ryou believed he was the real good guy trying to avenge his family. So much like the audience's point of view, we believed the Spirit was Thief King who wanted revenge, the only difference was we saw the big reveal - the Spirit of the Ring was never the Thief King, but the Big Bad using him as a puppet to revive himself. So somewhere during the manga, Ryou could have been helping the Spirit as an ally, or I'm just talking nonsense ;p
 * In the beginning of the Millennium World arc, Bakura takes back the ring from . Now, if the evil spirit is contained in the ring, how is he controlling Ryou to take it back? Further more, by this point he at least vaguely realizes that whatever is in that ring likes to possess and use him to be a Big Bad and therefore he should probably stay out of contact with it. This troper seriously doesn't believe Ryou is as much of an Innocent Bystander as he'd like the people around him to think.
 * Yami Bakura has been shown to be capable of putting a fraction of his soul in Yugi's puzzle. It's certainly possible that he left a fragment or more of his soul in Bakura's body.
 * At the beginning of that episode, there's a scene where Ryou is trying to escape Bakura's spirit (or something) by hiding in a church. Bakura then says that the two of them still have a mission to complete. And (quoted from the 4kids version) Bakura says "Does the term 'millennium items' sound familliar? You promised to help me obtain all seven." Ryou knew what Bakura was planning all along and had promised to help. If Bakura had forced Ryou to promise to help, then don't you think Ryou would have mentioned something about Bakura's plan to Yugi by now? Yugi had the Millennium Ring, so Bakura couldn't have controlled Ryou in order to stop him from telling Yugi without someone noticing. After Bakura mentions Ryou's promise, he takes control of Ryou. It's not the kind of thing he could do in front of Yugi without Yugi noticing. Going back to the "Bakura and Ryou have some kind of twisted friendship" theory mentioned above, I'd like to suggest that maybe Ryou had Stockholm syndrome for a while, and that's why he promised to help Bakura.
 * Why is he hiding in a church? Answer: he's possessed by a demon and he's hoping that the church will provide him sanctuary, or that there will be someone there who can exorcise it. The demon, however, manages to break his will by reminding him of the promise he was tricked into making that got him possessed in the first place. It doesn't matter what the evil spirit told him he was going to use the Millennium Items for, or even why Ryou agreed to it; all that matters was that he gave his consent to the evil spirit to use his body, and that consent, once given, cannot be revoked by force of will alone.
 * Another possibility is that he was somewhat resentful of his situation in the beginning (though this entire conversation is presuming we're ignoring the original series, where he explicitly tells Bakura to get out of him upon finding out what the ring is and what it does), but quickly realized what Bakura was actually willing to do, and got cold feet. By Season Five, he's definitely regretting his 'choice', considering he was obviously terrified out of his wits during the scene at the beginning of episode 199. Also, you're basing that 'promise' on the dub; in the original, Bakura merely says that Ryou has a 'duty', possibly implying that he considers it Ryou's duty to serve Bakura's interests as his host/hikari/whatever. Also, after Ryou wakes up in episode 220 in the original, after Bakura ditched him to go into the Memory World, he says he was 'chasing something' (possibly a dazed memory of running away from Bakura, or could mean that he was chasing sanctuary), then blacked out. That particular line would support the most common interpretation of the two; that Bakura suppresses Ryou when he takes over.

Millenium Magic may still exist in a lesser form

 * Judging by the amount of gold in furnace and the amount used to cast the artifacts, there should be a significant amount of waste metal containing bits of 99 souls lying somewhere in Egypt or other parts of the Sahara Desert. This waste alloy may lack the extra enchantments used to create the items but I think that the Shadow Games have a chance of a coming back should a greater magical force supplement the exist magic in the waste material.
 * Off to write a fanfic using Duel Discs that have pieces of Millenium Magic-ified gold in them...

Rex Raptor will grow up to be Chester A. Bum.

 * They both have orange hats as well as long, scraggly brown hair, not to mention Rex's vest is the same color as Chester's coat.
 * Well, there is a special from Yu-Gi-Oh Abridged, wherein Rex and Weevil watch Silent Hill and comment on it in a MST3K-ish fashion. And considering a WMG that says that the abridged version is actually the canon...

The Shadow Games/Games of Darkness/whatever the fans are calling them this week were created by Sigereth in order to further the Reclamation.

 * Sigereth, for those unfamiliar with Exalted, is a powerful demoness known by the sobriquet of "the Player of Games". As the title implies, her powers revolve around challenging people to games of chance and/or skill for ridiculously high stakes--think memories, skills, you body and soul...Sound familiar, anyone? Demons in Exalted are basically Sealed Evil in A Can--and the only way to break the seal for good is to corrupt the mortal realm until it's indistinguishable from the demonic one. Accordingly, Sigereth introduced the Shadow Games to the Yu-Gi-Oh world, knowing that the immense power inherent in them would be an enormous temptation to anyone who knew of their existence. The scary part is, her plan seems to be working--the Yu-Gi-Oh universe is getting steadily Darker and Edgier with each new installment, and this seems to coincide with how widespread Duel Monsters becomes among average people...

The Musician King is a rejected Guitar Hero character
He was originally going to be in Guitar Hero III as the best character, but The God of Rock replaced him. The King used his Iron Man time travel powers to find another game. He settled on Yu-Gi-Oh, but he lost control of his powers and continued to go back, winding up in the Yu-Gi-Oh anime and trading card game. Because of his cheating, he ended up stuck as the fusion of Witch of the Black Forest and Lady of Faith.

Atem only really cares about Yugi
The only person Atem ever actually cared about was Yugi, whom he cared about a lot. He only kept the others from getting hurt because their being hurt would hurt Yugi. When one of his "friends" is captured he gets serious and down to business reassuring Yugi it will be alright but when Yugi is captured he totally loses it and Yugi's the only one he really says goodbye to at the end. Also he was more interested in beating the bad guys to keep them from hurting Yugi than in saving the world. It always sounds a little off when he mentions the saving the world.
 * I'd buy that. Word of God has it that Yami was pretty evil to begin with (and the way he acts in Season Zero supports that idea) but Yugi just "rubbed off on him" somehow until he mellowed out enough to start being nicer, but it's very believable that Yugi's simply a Morality Pet of sorts and the only one who's really important to him... Though, then again, by that same logic, it was Yugi's relatonship with his friends, not specifically Yugi himself, which influenced Yami's change from Heroic Psychopath to a guy with only the occaisonal bout of What the Hell, Hero? syndrome. So... maybe they at least influenced him, I dunno.
 * Really, it's just likely that he's much closer to Yugi: they do, after all, share a body and the term "Soul Mates" isn't too far off the mark. Few people admit to having "favourite" best friends, but I reckon a lot of people with anything approaching True Companions do.

Atem and Yugi are in fact two halves of the same whole.

 * This was explored by Le Diz in her fanfiction, Akh. In which she dealt with the concepts of the Egyptian Ka and Ba: which are two different parts that together with a bunch of other bits make up a human being?s mind and body... (I think that Ka was the soul while Ba was the physical essence, but I may have that backwards). The original Pharaoh from 3000 years ago was a whole being, made up of both a Ka and a Ba, but when he gave up his life to save the world, his spirit separated and was sealed within the Millennium puzzle ...Or at least a part of his spirit was. The problem being that you can?t seal a physical body into a piece of metal so Atem?s Ba (or Ka, whichever) was left outside while the other, spiritual half was sealed within the puzzle. The Ba of course died straight away without a soul to complete it. But the clencher here is that rather than vanishing altogether, it reincarnated again, and again, and again. The first time it was probably still too weak to survive ? the newborn Ka-less Ba's would?ve been cot deaths, or else died very young ? but eventually, after millenia worth of reincarnations gradually getting stronger and stronger, the Ba became strong enough to exist on its own. That Ba is Yugi.
 * What this says about Atem (the Ka) going back to the afterlife without Yugi (the Ba) is anyone?s guess, though this troper would like to think it doesn?t matter since the whole story was about Yugi learning to be indepdent and that should still apply, whether he?s half a soul or not.
 * Also by this logic, Yami Yugi is probably not really Pharaoh Atem, since Atem was a combination of Ka and Ba, and if Yami is only one of those two....
 * Alternately, rather than splitting into Ba and Ka, the split was the Light side of the soul and the Dark side, which is why Yami was so evil when he was first unleashed, and Yugi was so ridiculously nice and naive. Eventually the positive and negative emotions bled over into one another, enabling Yugi to be aggressive and better understanding of if people are trying to take advantage of him, and Yami became more gentle and kindhearted. That's why Yami could move on- Yugi had become whole due to the time with Yami, and so Yami could move on to the afterlife, as the split was more even rather than +/-. Presumably, when Yugi kicks it, the two will reunite before the next reincarnation.

Duel Monsters is just an ordinary game
That is, until Haruhi Suzumiya played it and fantasized about the game being played by Magical Egyptians.

Duel Monsters wasn't started by the Egyptians, but are rather the manisfestations of magic shared by many different civilizations.
In 5D's the Immortal Earthbound cards are based on monsters from South America. Anyone could have made cards based on the Nazca Lines, but just like with the Egyptian God Cards, the Immortal Earthbounds must have their power from a higher magical source. Dartz from Atlantis, which existed before Egypt, also knew about Duel Monsters. And what about the kingdom that Yubel and The Supreme King lived in?
 * Egypt likely mastered Duel Monsters, at least based off Shadow Magic. The Doma Arc revealed there was an entire dimension of them, and would've been used by previous civilizations. The Egyptians merely manipulate Shadow Magic, and create monsters through this.

Alternately, while it is based upon the Egyptian method of sealing magic, Pegasus enchanted the game so it absorbs all kinds of magic.
Same as above: Egyptian, Atlantean, Japanese (the spirit monsters), Mayan, Alien (The Light of Destruction and Neo-Spacians, via the inverse of Clarke's Third Law) and whatever the hell culture Yubel comes from are all part of the game. While it was based upon the way the Egyptians seal up magic while tapping into part of their power, Pegasus figured there may be more evil wizards out there, so he made it so the cards absorb and dampen magic. This gives people a fighting chance against them. Ra used to be able to destroy a whole city. Now he can put one person into a coma at a time. It may be weakening, though, judging by the devastation the Earthbound Gods make when they are summoned. That's also why, when Yugi starts playing Duel Monsters, he no longer challenges other people to other games like he used to: he can't.

Duel Monsters is an antediluvian game played by Atlantis
Building upon the logic above, Duel Monsters or a form of it was played in Atlantis. When it collapsed the post-flood cultures that use pyramids and other Atlantis motifs, such as Egypt and South America, played the Atlantis game of Duel Monsters.

How the Millennium Ring Came Back
So how did the Ring come back after Tristan threw it? No One Could Survive That, right? Wrong. If you notice the Ring has five prongs that are strong enough to puncture one's chest, and Yami Bakura controls it. So its entirely possible that the Ring crawled to the castle using its prongs.
 * Facehugger Millenium-ring?
 * Or perhaps it mind-controlled Honda into thinking he threw the Ring away, but instead put it back on Bakura's neck.

Holographic games have eliminated the need for fused-monster cards
If you're using a computerized holographic system, all you need are the material cards and polymerization or a card of the same effect. Thus, why everyone seems to have every possible fusion card readily available- the fusion results are programmed in, rather than cardboard like the rest.

The Anime is Pandering to Kaiba's Fanbase
It would explain the increased amount of focus Kaiba gets, not to mention that two of the filler arc are focused around him. It would also explain Joey/Jounouchi's Badass Decay, as he is deliberately made to look even worse compared to Kaiba, such as him being made into the butt of a joke based on a card in Yugi's deck in one filler arc. It's almost like the writers have an ulterior motive as they make Kaiba look even more awesome while derailing his rival (besides Yugi) into a glorified Boring Failure Hero (Similar to what some fans believe Kishimoto is doing to Naruto in favor of Sasuke).
 * In fact, if you read the Millennium World arc, you will realize that
 * Insane Mass Guessing: The anime is pandering to Your Shipping Of Choice. This troper is sad that it is not true, especially with this troper's shipping--it seems to be the Butt Monkey of the Yu-Gi-Oh fandom.
 * Further Insane Mass Guessing: Little Kuriboh is a fan of Seto/Joey. "Love to love ya, baby..."

Yugi's appearance does not change when Yami/Atem takes over his body.
Which would explain why no other character really seems to question his new body/voice. The character of Yami only appears different so viewers can tell the difference between the two, and to emphasise how Atem is wiser and more confident than Yugi.
 * Except that in the manga, people actually notice that there's a difference.
 * This could be just because (as I think is remarked on toward the beginning of the manga) of the major difference in their expressions, posture, and voice--as a blindfolded Anzu said in the first volume, "Is that voice... Yugi!? No! They're similar, but too different! It's impossible! This voice is confident, not shy like Yugi's!" Remember, before he solved the puzzle, Yugi was a introvert whose only friends were the two guys who bullied him daily and a girl he spoke to every once in a while. Apparently he was so extremely shy that any display of confidence couldn't possibly be his doing.
 * Given proof in the very beginning of the Millennium World manga: when the gang question whether Yugi will be going to the museum after school. It's Yugi in control, and his posture is greatly drawn out (slightly straight back, both arms on his desk, feet firmly planted on the ground.) When he says "Why don't you hear from (the other me) for yourselves?" and switches control, the very next scene is Atemu sitting in a very different position from Yugi (slouching in his seat, one arm cast over the backrest, legs crossed and extended).

Mai really is terrible at Duel Monsters.
It's well established the she's a skilled and respected duellist-while she's still cheating. After she stops she has about two onscreen victories. The only reason she got so far in the tournements was because all of the good players were picked off by Yugi and Joey in Duellist Kingdom and by Kaiba and Odion in Battle City.
 * The trope Worf Effect exists for a reason. Have you actually paid attention to any of her subsequent duels? She loses them for bigger overarching plot reasons, in spite of dueling extremely well. One's skill is not determined solely by the end result.

Yami/Atem doesn't really look like Yugi.
I mean, anime-hair is one thing, but the tri-coloured spikes *from birth* is kind of pushing it. So, since Atem's memory is shaky at best, his physical appearance is always a combination of vague recollection and Yugi's looks, which he more or less pilfered as the first available source of inspiration. Even when we see Atem in flashbacks, he looks like that largely because that's what he thinks he should like - the change of skin shades was him remembering more of himself, but not all of the details. Same with Bakura.
 * Of course, this doesn't really explain the hair on the ancient carvings.
 * Who says it's hair? It could have been a fancy wig.
 * Regardless of if it was a wig or natural, it should have still been subject to gravity. I could maybe accept a handwave of Yugi's style being because of hair gel (or someone replaced his hair gel with superglue for a prank, as a friend of mine once joked) but I don't think Atem would have had anything back in ancient Egypt that could give either natural hair or a wig that much hold....
 * The Puzzle Did It.
 * The only problem I have with that is the flashbacks of other characters who didn't have their memories wiped, only sealed, also have this effect. Most notable is when Isis/Ishizu shows Kaiba some "visions of the past" in the museum. The ancient priest Seto goes through about 3 different hats in various flashbacks (not in the same episode) and Atem's outfit is different in several flashbacks as well. Not to mention that none of the flashbacks set in ancient EGYPT show the characters with tan skin. Aside from the Ishtars and Shadi, no glimpse of Egypt has the characters with darker skintones until the actual Memory World arc. And since Isis/Ishizu was using her Millennium Item to look directly into the past rather than having a flashback, I would assume her visions would be the most accurate. Instead they show a battle that never happened in the Memory World arc, complete with a character that seems to be an Egyptian version of Jounouchi/Joey that is never seen in Atem's actual memories! Personally I blame the series author. I think it's possible that he didn't have the characters' Egyptian appearances set in stone at the time he drew those scenes, and by the time the actual Memory World arc came around the character models had changed and he had scrapped the Egyptian Jounouchi/Joey.
 * ...Actually, A Wizard Did It might be the most likely explanation. The Memory World game at the end of the series was implied to be rewriting history (Zorc was attempting to retcon his original loss), and it might have written in Yugi's hair as the Pharaoh's hair as a side effect! And the reason all the flashbacks are different is that the ripple effects of history shifting around were taking effect very slowly.

Honda is Arnold J. Rimmer in a previous life

 * Though I have a hard time imagining what Honda could possibly have gone on to do that he'd deserve to come back as Rimmer.

Thief Bakura was an albino.
He used paint to keep from getting horriffic sunburns as a result of living in the desert.

The Shadow Realm is Limbo.
Or at least part of it. Why else do the priests go there instead of dying, yet we clearly see them "die". Whenever you exhaust your ka, you are unable to go to the Underworld so instead you wait it out in the Shadow Realm. As for Zorc, he was the Guardian of Limbo and wanted to bring the entire world into it, which would allow him to kill everyone there and trap them there.

Atem was highly skilled in combat before he died.
And despite the memory wipe he still retained some of those skills. There's a saying about riding a bike. Once you learn how to do it, you never forget. Perhaps combat is similar. Physical combat requires being able to think on your feet and using strategy, and even without his memories Atem is certainly capable of both of those skills. Plus in the dub when giving Joey advice against Mai, he says that "She is just trying to divide and conquer, a strategy that's been used for centuries...believe me, I know." But there's also evidence for the physical combat as well. Dueling on a blimp with icy winds? He can take it. And in the Kaiba Corp tournament in season 5 when the computer traps them inside a building, he does some rather show off-y leaps onto and off of the dueling platform. And of course, who could overlook a nearly EIGHT FOOT HIGH vertical jump and a Link-esque tuck and roll he pulls off in Capsule Monsters? Of course, Your Mileage May Vary on that last example depending on what you consider to be canon. Also, in ancient times it was fairly common practice for royalty/high ranking officials to know self defense at the very least. In the Memory World arc there's a brief flashback of Priest Seto and Akhenaden sparring with swords, and Atem himself is shown briefly wielding a sword while on horseback in the anime, making short work of Bakura's henchmen that had dealt with some royal guards fairly easily.
 * Historically, Pharaohs were war chiefs as much as administrators and religious leaders. And in ancient times, the general led from the front. Atem having combat training makes perfect sense in that context. And it's pretty obvious that he was very fit. Combat training from a young age would explain that. (As would being very rich, and thus having access to good food, in the days before burgers.)

Atem could potentially be brought back/revived for a future sequel
Humans shed dead skin, and they shed a LOT of it. We shed roughly 4 kilograms per year. Atem's shown to have had the Millennium Puzzle for several years before his death, and hygiene back in those days was almost certainly not as clean as today's standards, so it stands to reason that the little box the Puzzle's pieces were found in may contain some 'dust' that is actually made up of Atem's shed dead skin cells. If technology became advanced enough, and if that dust was still around, and IF those cells still had viable DNA...it would potentially be possible to bring Atem back by creating a clone. Although how that would deal with the whole issue of his spirit being in the afterlife, I have no idea since I'm not an expert on the Egyptian Afterlife and cloning. It might make for a very interesting plot if they ever made a sequel like this.
 * I'm pretty sure that after 3,000 years there wouldn't be any viable DNA left. On the other hand, the stuff Kaiba does with holograms probably isn't possible either, at least with today's technology.
 * There have been a few Egyptian documentaries where they successfully get DNA from mummies such as ol' Tutankhamun with today's technology. The series never really gives much hint about the level of medical and genetic technology, but if it's on par with the hologram and computer tech...all they'd need to do is be able to clone stuff and find a DNA sample.

Marik was supposed to marry Ishizu
Think about it: Tombkeepers are not allowed to set foot on the surface, so how should they ever be able to meet a woman that can become their wife and give birth to a son, that will become the next tombkeeper?

The only way to have children without breaking a thousand year old tradition would be marrying their own sister (or even mother?)

Considering that Brother-Sister Incest was no taboo in ancient Egypt and often practiced in the royal family, is definitely possible, that Mariks father planned to marry Marik/Malik of to Ishizu/Isis.
 * If that's true, then Marik/Malik and Ishizu/Isis shouldn't be as...normal as they are. 5000/3000 years of family inbreeding is NOT good for a gene pool. Although it might be possible that a recessive genetic disorder contributed to the psycho that is Yami Marik/Malik. It's also made more likely by the fact that in Ancient Egyptian tradition, lineage was inherited from the mother's blood, not the father's (at least when it came to royals). A man had to marry a princess to have a claim to the throne, which is why so many pharaohs ended up marrying their sisters/half-sisters. So this would probably also mean that Atem was married to his sister/half-sister back then too....
 * They had possesion of a magical artifact. I wouldn't be surprised if the Millenium Items removed any genetic disorders.
 * Another thing is that, in some ancient cultures, if a man wanted a woman to marry him, and she was unwilling, he would just rape her. This would allow him to "claim" her as his wife, since no one else would want her. Why the hell would Marik's mother have married a man like her husband, unless she was forced to?

Duel Monsters was created to teach children about the value of friendship.
And the only person who understands this is Tea, thus explaining her obsession with The Power Of Friendship.

Honda and Jounochi didn`t become Yugi`s friends out of their own free will
Remember that Crowning Moment of Heartwarming in the very first chapter of the manga where Yuugi wished on the Puzzle for "friends who would never betray" him? And then Jounochi and later Honda, who bullied and mocked him before, become his friends. Sounds sweet, right?

Only until you think about it for a while and realize that they must have been brainwashed by the Puzzle to make friends with Yugi. And to be absolutely loyal to him. Well, Jounochi did bring back the puzzle piece he stole before the puzzle was completed, but even then it could be strongly considered, that he was mindcontrolled by the piece, which used him as a tool to become reunited with the rest of the Puzzle. And even Anzu, who liked him before, didn`t seem to be a really close friend to him (at least not as close as later in the manga/series), so even she might have been brainwashed. The Fridge Horror goes even further. The complete quote is: "Friends who would never betray me and friends whom I would never betray" So maybe the puzzle even brainwashed Yugi himself to become absolutely loyal to his new "friends". This makes the whole "Friendship is the best thing in the world" message of Yu-Gi-Oh a bit icky.

Duel Monsters holograms are voice-activated.
Why else would they yell about every move they make?
 * TECHNICALLY, you're supposed to say what a card does every time you use it, in case your opponent isn't familiar with the card (it's sometimes hard to read an opponents card, since it's upside-down to you). The yelling is just Rule of Cool.
 * The distance between duelists using Duel Disks or the Duel Arenas is enough that you'd have to yell just to be heard. Otherwise, yes, it's Rule of Cool.

After Zexal there will be another serie...with a girl as the main character
It's not the first time they try to attract the female public with that old trick...unless Yuma is a girl.
 * If they do another crossover movie, the other 4 main characters will lampshade this.
 * Do they even NEED a girl as the main character to attract female fans? I doubt it. All my female friends who like this series enjoy it for one reason: THE MEN. Just look at Otogi/Duke, Bakura, and the Pharaoh himself. If they really want to get more female fans they need to either make new sexy characters (or bring back old sexy characters for that matter) and make sure that children's card games are not the main focus of the series. I'm not saying they should change it to a Romantic Plot Tumor, I'm thinking more...slice of life. Or more like the first seven volumes of the manga that Season 0 was based off of. The title, Yu-Gi-Oh!, translates as "King of Games" after all. Not "King of Card Games" or "King of Duel Monsters" or "King of One Specific Game and No Other". It's "King of Games". That's games plural, as in "more than one". Plus it was a little more identifiable with audiences, having a series where people actually got punished for bullying instead of getting away with it like they do in real life. Yet few people, if any, can identify with having to win a card game to save the world from ancient evil magic. (One of my friends loves to watch Season 0 and imagine that everyone who gets a penalty game is replaced with someone who used to bully her in real life.) Oh, and throw in a bunch of Shirtless Scenes or even some Walking Shirtless Scenes and you'll have the female fans hooked for sure.

Atem is one of Yugi's acenstors.
That hair has to be genetic.

Atem/Yami Yugi is NOT the Nameless Pharaoh.
In this scene from the manga, Isis/Ishizu states that the Pharaoh depicted on the Tablet of Memories is from the 18th Dynasty. In order to actually be in the 18th Dynasty, his death would have had to take place at least 3277 or more years before Yugi was born. The one thing that Yami Yugi/Atem seems sure of, even without his memories, is that his soul is 3000 years old. If we assume that Atem/Yami Yugi's account of how long his soul has been around is accurate, that would place his reign well into the 21st Dynasty and not the 18th Dynasty. If both Ishizu/Isis and Yami Yugi/Atem are correct, then that means Yami Yugi is from the 21st Dynasty of ancient Egypt and therefore cannot be the Nameless Pharaoh from the 18th Dynasty. This could imply that when Yami Yugi regained "his" memories, he actually ended up with the memories of a completely different person and now believes that he was/is the Nameless Pharaoh, which is why he was able to successfully use Atem's name to destroy Zorc in the Memory World arc because Your Mind Makes It Real.
 * This is just splitting hairs. 277 years difference isn't that much when you are counting in millenia. The Pharaoh was probably just rounding or estimating (it's not like they were using the Julian Calendar back then anyway).
 * True on the part of the calendar, but then this is wild mass guessing for a reason.

Yuugi suffers from a Napoleon Complex
That's why his hair is so crazy. He wears it all stuck up on purpose to make himself feel taller.

Yuugi died right after Yami left to the afterlife
Taking it further from the 'Yami and Yuugi are actually two halves that make one soul' (Atem) theory, if Yuugi was truly being reincarnated over and over again waiting for his other half to show up, then the point of this is for them to remain together, not for Yuugi to 'move on' with his life, seeing how he's only half a soul. So regardless of how much he learned from Yami, Yuugi can't (literally) live without him (and the other way around too); so it seems logical that Yuugi as a half soul would want to follow his other half, even if it was to the afterlife, so that, finally together, they can reincarnate one last time as a whole soul (Atem's reincarnation) and live the life that was taken away from them. This can also be supported by the fact that seeing how 'history repeats itself' (the whole Kaiba and Yuugi rivalry thing), just like Atem died and Seto was crowned the next pharaoh, the same way Yuugi died mere hours after Yami's departure, and Kaiba was 'crowned' king of games by default. The very last scene of the series is actually Yuugi reminiscing his time on earth. GX doesn't count.
 * Personally, I don't agree with the 'two halves of one soul' theory, but I understand the reasoning behind it and your WMG. Yet there is one glaring problem I see and would like explained. Egyptian religious practices regarding the afterlife pretty much required the body to remain in tact for the Ba and the Ka to live on after death. It's a big part of why they wanted to preserve bodies through mummification. And yet in every continuity of the manga or anime that I have seen, when it shows the inside of Atem's tomb there is no sarcophagus or anything else to indicate a mummy was ever there. (Here's the scene where Yuugi's grandpa finds the Puzzle several thousand years after Atem's death. Do you  see a mummy in that burial chamber?) So my problem with the theory is this: How could the Yuugi half of the soul have been reborn all those times without a body to keep the Ba and Ka 'alive'? I could maybe understand the Yami half surviving if his being trapped inside the Puzzle functioned as a type of magical stasis, but the Yuugi half had no such means to preserve itself. Thus shouldn't the Yuugi half of the soul have 'died' for real before it even got the chance to reincarnate once?
 * Unfortunately, Takahashi never bothered to get his facts right about Egyptian religion when doing the manga, so we'll never know what Yuugi actually is to Yami, seeing how he was only addressed as 'the destined vessel' during the series. But supposing that Takahashi knew what he was doing... what Solomon was looking for was the puzzle box, wasn't it? So the room that they're in when they find it could have been another chamber made solely to guard the puzzle, whereas the pharaoh's body was kept in another one.
 * I was under the impression that Solomon didn't know exactly what was in the tomb other than some 'fantastic game' that no one had beaten. Also, I could have sworn that at some part during the manga, Solomon called the room with the puzzle in it the burial chamber, but I can't remember where I saw it since my copy of the English manga seems to be worded slightly differently than every single online scan.

Mana is Atem's half-sister.
She's the daughter of one of the previous pharoah's concubines. It explains why she's always at the palace, and also says something about the lack of any Spare to The Throne.
 * If that were true, she'd be Atem's wife as well. The ancient Egyptians believed that royal blood was passed down through the mother's side of the family, so a king usually had to marry a royal princess in order to maintain a legit legal claim over the throne. And yet there's no evidence that he's married at all. For example, in that scene where he wakes up in bed (infamous among some friends of mine due to Atem being shirtless) it doesn't exactly look like he's leaving room for a second person who's just gotten up to use the bathroom or something.... Said friends and I think his dad was actually unable to have kids, and Atem's mom was an ancient goddess in mortal form who was able to literally godmod around the infertility thing. The goddess-mom idea is our explanation for why Atem seems so sexy, as well as why he appears to have no siblings.

Kaiba's got a thing for Joey.
Let's think about this for a moment. The last time Seto had any even halfway-normal social contact with his age group was when he was elementary-school age. He was then mentally and possibly physically abused into believing love and caring are weaknesses by his adoptive father. So what does he do when he develops romantic feelings for someone? He belittles and teases them like an eight-year-old with a crush, all the while mentally excoriating himself for being "weak." He continually wastes his valuable time mocking Joey, even going so far as to duel him when his brother is in immediate peril (during the Duel Kingdom arc). He may say that Joey's not worth his time, but it sure doesn't look like he always means it.
 * Add that to the few but noticeable Foe Yay moments the two get (chief among these: in the manga, Kaiba, not Serenity, saves Jou's life after his mind-controlled duel with Yugi in the Battle City storyline), the whole BEWD versus REBD thing, their Red Oni, Blue Oni relationship, all those nicknames (let's face it, "puppy" sounds more like a pet name than anything else, and even "mutt" is a bit...eh), and the similarities in their personalities, and it's a wonder this ship doesn't have more fans.

Atem is not in the Afterlife.
At the end of Atem's last scene, we see him walk towards the Afterlife, where all the other priests are. Mahado included. Now, who became the Dark Magician, again? Exactly, Mahado, who is still Duel Monster and not in the Afterlife. Where did Atem go is anyone's guess...
 * The people he sees in the afterlife makes that scene pretty confusing, seeing is half the people there either became duel monsters or got completely reincarnated. It's easier to think he's in the afterlife if you ignore that particular scene.
 * This troper's pet theory is that Atem went to the Afterlife of the past. Since then, Mahado went back to being the Black Magician and all the other priests reincarnated...which means Atem reincarnated into Yugi.

Season 5 is a Stable Time Loop.
When Bakura went back in time, it wasn't altering history. Rather, it was pre-ordained. Theif!Bakura discovered how to use Zorc because Dark!Bakura set him up for it. This is the real reason why destiny needs Yami Yugi to go back in time: if he doesn't, it'll break the Stable Time Loop, no doubt causing a reality-destroying Temporal Paradox. Neither side is aware of this Stable Time Loop. This is also why all previous villains were doomed to fail. Shadi is an agent of the timeline, to make sure it stays on track. And, like season 5, his beginning is his end.

The Millenium Items Power's are either Your Mind Makes It Real or Green Lantern Ring
Seriously, these things have tons of vaguely established powers, so it could fit either trope. For one things, the original powers of the items that were used 3000 years ago, to judge criminals and take their ka's aren't used in the present, but lots of other powers are, like Marik using the rod to mind-control people. Priest Seto sure doesn't seem to know that the rod can do that. Maybe it's because he didn't have a reason to mind control people, but Marik did, and Your Mind Makes It Real ? And then there's all the powers that get used only once, randomly, even when they'd be very useful at a later time, like Yugi's Puzzle's ability to 'put souls back into their original bodies' ? Where was that when the other Yamis kept showing up? And Bakura's ring's power to summon real duel monsters out of a duel and use their effects on people (the Man-Eater Bugs from season 1) ? That would have been useful later too (not to mention cool) but it only happens once.
 * Same troper again. I just started reading the manga, and Shadi's mind-control of Yoshimori and Anzu also fits here.
 * Seeing how Takahashi made tons of inconsistencies during the series (in the card game and Egyptian history/culture for instance) I would say that the power of the Millennium Items are random at best, is because the the author did whatever he did for convenience sake, and later forgot about what he had written. (Indeed, the soul switching thing would have been very useful during Yami Marik's duel).
 * Some of the things you mention don't happen in the manga at all. The puzzle was never used to swap Bakura and Yami Bakura, for example. They killed Yami Bakura in the shadow game, and then Bakura's avatar in the RPG was able to use healing magic to restore Bakura. Also I don't believe Yami Bakura ever summoned real duel monsters such as those Man-Eater Bugs (I could be mistaken, haven't read that part in a while). The powers of the items are a bit more consistent in the manga, so I think part of it can be blamed on Adaptation-Induced Plothole.

Cards in-universe are made of some sort of shape-memory plastic whose hardness can be varied by the users.

 * Consider than in the course of the various series, they've been used as throwing weapons, been immersed in water/dropped in the dirt, been bent at sharp angles, yet still remain pristine. This has been a Headscratcher for me for a while, but having them be made of a plastic that returns to form makes it make sense.

Time Wizard has an incredibly diverse array of attacks.

 * Joey never actually attacks anyone with Time Wizard in the series (understandable, since its ATK is a paltry 500), but I have a theory that the little fella has a different attack for every possible number that Magic/Trap/Monster effects can boost his ATK to (I know his powers, when shown, involve him aging the world around him, but bear with me here.)
 * 500 or below: He just conks the opponent with his staff.
 * Between 500 & 1000: Travels back to One Million BC; comes back dressed in a leopard-skin loincloth, holding a giant club that he conks the opponent with.
 * Between 1000 & 1500: Travels back to Medieval Japan; comes back dressed as a samurai, holding a katana that he cuts the opponent open with.
 * Between 1500 & 2000: Travels back to the Age of Sail and comes back dressed as a pirate captain, complete with an entire fleet of pirate ships training its cannons on the opponent.
 * Higher than 2000: Travels back to World War II and drops a nuke on the opponent.

Marik is a reincarnation of part of Priest Set's soul.

 * One thing that confused this troper was how Marik wasn't a reincarnation of anyone, despite both his siblings and his father having had past lives. Marik's father is CLEARLY Priest Akhenadem's reincarnation - they look identical, and they're both fairly evil - and Set was Akhenadem's son. Both boys use the Millennium Rod, and their facial features are quite similar. Also, in this universe, souls are made up of different sections. It's not too hard to imagine part of Set's soul coming back as Marik.

Rebecca's PHD thesis will be on Duel Monsters throughout the ages.
First, she's the granddaughter of an archeology professor, and she's in college by 13. From a background like that, graduate school is a no-brainer, especially since no one is going to hire a 16/17 year old for any serious work due to child labor laws. So, she decides to follow in her grandfather's footsteps and become an archeologist.

Her first paper was on that whole Atlantis fiasco, which would have gotten her laughed out of any self-respecting academic institution but for the fact that she could produce corroborating evidence. After Zero Reverse, she went to South America to perform a detailed study on the Nazca Lines. By the time she publishes her thesis, people have already begun to take the prospect of Duel Monsters being ancient and supernatural seriously (they are, after all, attempting to harness their supernatural properties to power reactors), so she does pass her dissertation defense (cue PhD in dueling jokes.)

The reason Atem uses the Seal of Orichalcos against Rafael is that he was wearing the Orichalcos stone fragment around his neck at the time.
That explains not only why he used it, but also how Rafael knew he would use it. It has nothing to do with his character and everything to do with the fact that the stone was manipulating him.

Bakura's parents are Milo and Kida
Just try and prove this one wrong!
 * Gladly. Milo wouldn't see a reason to leave the city or move to Japan.

Monsters with over 2000 attack are extremely rare before and during Duellist Kingdom
In the real world card game, monsters with more than 2000 attack are pretty common. Throughout Duellist Kingdom however, we are treated to people acting as though Yugi's Summoned Skull and Dark Magician are all but unbeatable, Mai powering up her Harpies to 2450 is made out to be an enormous deal, and Joey's Red-Eyes (a pretty average 7 star) is used almost as effectively as Kaiba's Blue-Eyes when the heroes need a beatstick. Even Bandit Keith, the American champ, uses the Slot Machine (which at 2000/23000 is a pretty weak 7 star) as his trump card. The obvious conclusion is that Pegasus only manufactured a small number of cards with more than 2000 attack, and a tiny number with over 3000. That's why even the best duellists will only have one or two monsters with those kinds of stats, and the mere possession of a creature with over 3000 (Kaiba's Blue-Eyes, Weevil's Perfectly Ultimate Great Moth, Yugi's Black Lustre Soldier) is a mark of status.

An idea on Atem's ability to control destiny
At first I thought it was some sort of limited reality warping power. Now I think it might be possible that his ability stems from Quantum Theory. The double-slit experiment demonstrates that we can alter reality just by looking at it. Taken to its logical extreme, it should be possible to change an event (such as a card draw) just by willing it. This would be "controlling" the outcome of the event and therefore "destiny" as well. Alternatively, he could be using magic to augment the effects of Quantum Theory rather than just using an extreme form of Quantum Theory.

Mai and Cyndia/Cecilia were sisters
They look extremely similar and both have a connection with Duel Monsters. Basically, Mai only switched to Duel Monsters from other card games because her sister's boyfriend/fiancee/husband invented them. She doesn't say anything about it because she's too proud to let anyone think she's only good because of her connection to Pegasus, and he doesn't say anything about it because Mai asked him not too. As a corollary, if Pegasus finds out that Panik attacked Mai, what Yugi did to Panik will look like a walk in the park.

Pegasus put microchips in the cards to limit counterfeiting.
If the ones that came out before the holographic and machine-dueling devices were planned didn't have chips, that should have come up during the tournament. Pegasus put chips into the cards that would tell readers at tournaments if they were real, and the non-matching ID codes in the chips or lack of chips altogether would have identified them as false. The counterfeiters in the Battle City tournament and later found a hole in the security, which let certain "null" ID codes in, and allowed them to tell the machine that their "blank" card had the same name, stats, and display as a real card.

== Pegasus put microchips in the cards because he expected the Internet and internet-based peripheral devices to have a massive boom in the late 1990s and after the turn of the century. == With as many cards as there already were and eventually would be, and how popular the game was expected to be, manageable codes would eventually run out or people getting codes online would be able to flood the online market with virtual rare cards. If they used ID chips, there would be a 1:1 ratio between real and virtual cards. It wasn't a perfect solution, but without requiring online validation of the cards during every trade to make sure someone didn't trade or sell the real and virtual copies to separate people, it was probably the best solution available.

The Millennium Puzzle doesn't actually grant wishes.
Yugi only believes that it does due to a misinterpretation of the inscription on the box.

Yugi's wish for friends couldn't have been granted by the Puzzle, since Jounouchi's first act as a friend was to give him the last piece, meaning that they were already friends before it was even solved. At one point, Yami even says that Yugi made those friends himself, and it wasn't only because of Yami. Yugi's second wish, to see Yami again, was the natural consequence of solving the Puzzle and therefore didn't need to be granted by it.

Insector and Dinosaur are stage names.
Haga and Ryuzaki aren't legally named Insector Haga and Dinosaur Ryuzaki- they're just using stage names that sound cool and complement their decks.

There is a Blue-Eyes Four-Headed Dragon.
At the start of the show it was stated that there were 4 Blue-Eyes White Dragon cards in the world. Kaiba then proceeds to destroy the one in Granpa's possession, leaving him as the sole owner of the remaining three BEWD cards, as well as their fusion card, Blue-Eyes Ultimate Dragon. Now, say he had taken the fourth card instead of destroying it. Do you think the show's creators would not have introduced a fusion between all four?

All said and done, it's actually kind of scary that the 4-headed card will never get to be played.

But only 3 of the same card can be in your deck(Kaiba says this is why he tore up the fourth one, so it couldn't be took and become an enemy), so how would he get to fuse all 4 if he could only have 3? Maybe it could be a fusion of the Ultimate and Shining Dragon.
 * Kaiba's Clone Dragon could be used to make a 4th Blue-Eyes.

Exodia is unlimited in the show
The reason is because it's so rare that the banlist creators thought nobody could get more than one of any piece, so they didn't bother restricting it.

Noah Kaiba is now a Net Navi
He said for Mokuba not to worry about him, and he displayed an ability to control the computer systems from inside. He uploaded his brain to the internet and now he challenges people to duels forever on [http:www.DuelingNetwork.com Dueling Network].

Yami Yugi/Atem lost to Zorc the first time and was traumatized by it.
Why would he need to seal himself, his memories, and the Big Bad away for 3/5000 years if he'd won? The answer is Atem didn't win at all: the whole sealing thing was to put Zorc's plans of destruction on hold until Atem was ready for a rematch. As for the trauma, while during the series Yami doesn't remember losing to Zorc, he has a very consistent reaction when in duels. If it isn't a duel just for fun and Yami starts losing, he panics. The biggest example is when he played the Orichalcos. Not only was it unnecessary - he had the cards in his hand to last at least one more turn - it ended up costing him the duel and Yugi's soul. Even if Yami had still lost, as long as the Orichalcos hadn't been played then nobody's soul would have been taken at all. Even in non-filler duels, Yami always seems to need Yugi and/or other people goading him to keep going once he thinks he's going to lose...otherwise he freezes up.