Ben 10/WMG

The Omnitrix/Ultimatrix is a prototype for the Animorphs Escalin Device
Or the Escalin Device is a prototype for the Omnitrix - either way, they're related. Think about it: both are forms of alien technology that absorb DNA and allow the owners to morph into different creatures (there's no evidence to deny the fact that Ben could turn into an Earth animal if he wanted to.) Both have time limits of different sorts as well.

Ghostfreak and Doctor Victor were working for Eon.
Ghostfreak wasn't out of the Omnitrix long enough to put any sort of plan in motion and certainly wouldn't have been able to communicate with his three henchmen during the time he was loose during "Ghostfreaked Out"; the events of the episode took place over a single day, and he was shown constantly chasing Ben. Eon was shown in the Live Action Adaptation Race Against Time to have knowledge of the Omnitrix, including its ability to absorb the DNA of aliens. He could have planted Ghostfreak there. In addition, he is shown using purple energy, and along with the Omnitrix absorbing DNA, the telltale sign of season three's arc is purple lightning that looked rather like the purple electricity crackles that were seen in the clock gears during several Race Against Time scenes. Thus, it's likely these are more than recycled plot elements; they're continuations of the same arc, and Eon was its Big Bad all along.

The Omnitrix has a measure of life, sentience and Genre Savvy, and is training Ben.
Think about it. Ben would go Fourarms every other time if he could. The "accidental" mistransformations (which have never been potentially lethal, like getting Ripjaws in Arizona) force him to think innovatively, or at all. It also times out inconveniently (more adaptability training), and recharges just in time to protect him and others (preserving the host). Further, it seems to take opportunities to evolve when they appear (gathering more aliens, and its "grown" form in Ben 10,000). Ken's Omnitrix ("Ken 10") is the (asexual) offspring of the original, since Azmuth probably wouldn't make another. He probably didn't even realize what he had created the first time around. Since there's at least one technological non-human species (Galvinic Mechamorphs like Upgrade) in the Benverse, it's plausible.
 * Acutally, "Ken 10" with commentary stated that Ben used the combined smarts of Grey Matter and two other aliens to create another one.
 * Alternatively, while the Omnitrix does possess partial sentience, it's just annoyed at being stuck to the wrist of a ten-year-old brat and does everything in its power to mess with the kid unless its own existence is at stake. (It was uncharacteristically helpful during "Secret of the Omnitrix", for example).
 * The "Ripjaws in the desert" thing happened in the fourth season. It didn't become an issue because Ben hijacked another RV's bathtub.
 * The Omnitrix occasionally extends its timing-out sequence longer than usual. This usually prevents Ben from dying or having his identity discovered. It does not, however, keep him from losing battles or reaching destinations safely.
 * In addition to all of the above, the Omnitrix is in love with Ben. It chose to bond with Ben, after all; there was no reason for it to jump out and attach to his wrist before he even touched it. Then notice how, after he developed his crush on Kai, it inexplicably refused to let him turn into Ripjaws to save her from a flood . And in Alien Force, the annoying beeping that made the Upgrade think it was a Plumber communicator started when Julie looped her arm through Ben's. Why Asmuth programmed it with the personality of a Clingy Jealous Girl is anyone's guess.
 * The werewolf episode with commentary states that the reason he couldn't go Ripjaws is because the Omnitrix was somehow stuck in between "Use" mode and "Collect" mode at the time. Why Ben doesn't have to switch it to collect mode for the rest of the aliens he absorbs later is beyond me.

Ben and Gwen are brother and sister.
This is almost text. They have the Sibling Yin-Yang thing going on and even share the same birthday! Grandpa Max split them up amongst his own kids to give them disparate upbringings to prepare for their inevitable destiny.

Ben and Gwen were meant to breed.
Taking the above theory a step farther, the reason Grandpa Max split them up was to avoid the "Westermarck effect" and the summers together were a ploy to create a little Belligerent Sexual Tension early and progress from there.
 * Why he would do so, is a bit of a mystery, however, given that he was a Plumber, he probably has reasons that far outweigh any cultural taboos against incest, and this is likely not the worst, or most morally Grey thing he has had to do for the Greater Good.

The reason future Ben has no sense of humor and is much more of a Jerkass in "Ben 10,000" is that he had recently lost his wife, possibly in battle.
Think about it. The episode "Ken 10," set seemingly 10 years later than "Ben 10,000," features his son, but no mother of this son appears or is even mentioned. Ben's often a Jerkass, but his losing his sense of humor is a definitely a personality departure, and this would explain why he was so insistent on trying to keep track of all Earth crime and solve it himself - guilt for not being able to save his own wife/lover. Especially if he witnessed her death first-hand. Ken not appearing in this episode doesn't conflict with this episode because "Ken 10" is never said to be exactly ten years after "Ben 10,000"; this gives some leeway, allowing Ken to have been born and his mother to die shortly after.
 * Disproved in the special version with the comments. It says that Ben eventually marries Kai (from the werewolf episode) and that's she's just off somewhere else.

Future Gewn IS Ben 10,000's wife/lover and mother of his child, or at least, in one timeline/reality.
As above, asides from the special version with comments, Ben doesn't seem to have any other woman in his life.

Future Gwen is dead and is a ghost.
Taking the theory that something tragic happened to Ben's significant other (if it was Gwen) Gwen being dead would explain a personality shift.
 * Also, she seemed slightly translucent...
 * There's also the floating thing...
 * And phases through solid objects...

Kevin 11 is the nephew of Peter Petrelli from Heroes.
They're both Emo kids from New York City with power-absorbing abilities, and both fight a DNA-stealing arch-enemy with a watch motif.
 * Nathan's been even busier than we thought.
 * In that case, Julie is somehow related to Hiro.

Alternatively, Kevin 11 is an alt-universe version of SYLAR.
Teen Kevin and Sylar look somewhat alike, and Teen Kevin even wears the SAME outfit Sylar wore when traveling with Suresh in Season 1. (The only thing missing is the Ramones logo on his black T-shirt.)

Both apparently have a core superpower that allows them to steal the superpowers of others (Kevin starts out by stealing powers from Ben's 10 aliens, and Future Kevin from "Ken 10" had apparently spent years upgrading himself by stealing DNA from assorted Null Void aliens); yet the writers seem to underuse this in favor of sticking to a single all-purpose power (Telekinesis for Sylar, Absorbing Man-Lite for Kevin).

Both apparently have major step-parent issues. Finally, both have recently gone through rather abrupt, fairly out-of-left-field Heel Face Turns (although Sylar seems to have gone back to amusingly murderous sociopath).

"The Storyteller" is The Monitor.
Ben 10 is a multiverse spanning narrative. Episodes switch from parallel Earth to parallel Earth to suit whatever yarn "The Storyteller" (the voice we hear in "Gwen 10" and "Goodbye and Good Riddance") chooses to spin. This would explain the the mix of continuity changes between the original series (and certain original series episodes such as "Gwen 10" and "Ben 10,000") and its spin off properties "Ben 10:Alien Force" and "Ben 10: Race Against Time". This would also explain the Omnitrix's similarity to the Dial in "Dial H for Hero", the Dial is the DC Universe's equivalent.

Alternately, Paradox is "The Storyteller" trying to find the best possible future
Paradox(Ben 10: Alien Force) is watching/affecting multiple possibilities in order to reach the best conclusion. He convinced Future!Gwen to retrieve Ben because it was one of the best ways to alter the prime timeline without introducing himself to Ben before it was right.

The Omnitrix does not "time out" or need to "recharge."
In addition to the dial, the Omnitrix is triggered by changes in its host's willpower or emotions or state of mind that Ben just hasn't figured out yet. This makes its bond with its host stronger; it was after Ben accidentally turned off this function (so he could "go alien" completely at will) that Vilgax was able to remove the Omnitrix.
 * Willpower as fuel? Then that means...

The Onmitrix runs on Spiral Power.
All we need now is Way Big wearing Kevin's car as a hat (for the Shout Out to Megas XLR) and yelling "JUST WHO THE HELL DO YOU THINK I AM?"
 * Does this mean Verdona is an Anti-Spiral? And that Gwen, by association, is Nia?
 * Sure, why not. And while we're at it, Vilgax is Lord Genome.
 * So the self-destruct on the Omnitrix is basically the Spiral Nemesis?
 * Pretty much. However, who is Kamina? Kevin strikes me more as a sort of violent Rossiu. Wait, I got it: Ben's Aliens are TTGL characters.

Everything after "Perfect Day" is dream of Ben's.
At the end of "Perfect Day", Ben (as XLR8) attempts to put Enoch into the dream machine but fails; Enoch puts Ben in the machine instead, slaps on the Omnitrix, and transforms, only for it to be revealed that Ben put Enoch in the machine after all. That, however, is what Enoch wants Ben to think, that he's succeeded. What really happened is, Enoch has put on the Omnitrix and taken care of Grandpa Max and Gwen, and now the Omnitrix has fallen into the hands of evil.

Ben 10 is a comic, and Gwen wrote it
"Gwen 10," "Ben 10,000," and "Goodbye and Good Riddance" "clearly" reveal that the events in the series takes place in a comic book series. Gwen is (arguably) a Canon Sue. Do the math. Ben 10: Alien Force as an Alternate Continuity makes more sense. It is written by Kevin Levin, who has a crush on an older Gwen. And who wouldn't?

Grandpa Max is Mighty Max
Think about it. Max lost his hat at some point in his near past forcing him to start a new life, but what is a former time and space traveler to do? Join a government organization that would benefit from his experience of course!

The Sumo Slammer games made by the Government
The Feds manufacture the game in order to disguise the passing of information from coast to coast. Besides why else would that warehouse in "Kevin 11" be so heavily guarded?

The Omnitrix is an upgraded adaption of the Element Of Power/Wotnot Book (from Kameo: Elements of Power)
The similarities between the two devices are unmistakable. Both can transform into 10 useful creatures, each with a Meaningful Name. The transforming devices are small, round, colorful objects resembling jewelry. The method of selection for which creature to transform into is a circular "wheel" for both. After absorption, both devices add that creature to the transformation wheel.

The Omnitrix is the better version because of a wider variety of creatures--Stinkfly, Ghostfreak, Overload (was that its name?) whereas Kameo's warriors are limited--no method of flight, most prominently. Secondly, Kameo's device is in two parts, and larger. In Kameo's universe, "Gods" gifted the wotnot book, but Sufficiently Advanced Aliens are mistakable for gods. The Element Of Power was a test run. Also, some ideas are reused--Rubble and Fourarms have a very similar head shape, and another telltale clue--there's only one creature that uses a ball(s) in each. Ben 10 has XLR 8; Kameo has 40 Below. Oh, and those are the only creatures that have a number in their name.

The Omnitrix was trying to kill Ben
Everytime the Omnitrix "timed out" at the most inconvenient time, or changed Ben into the wrong alien instead of the one that could get him out of that specific situation, the Omnitrix was deliberately trying to get Ben killed. Why? Because the Omnitrix knew that it wasn't supposed to attach to Ben. The only reason it did at the time was because it was acting on instinct and it needed a way to get to it's true host. Unfortunately, the only way it could detach from Ben is if he died. So it keeps trying to kill him so that  can get it. But everytime the Omnitrix tried this, there was the risk of it falling into the wrong hands, so it decides to "work" again in order to save itself, and then try again another time.

The cartoon is an adaptation of a comic book
In a parallel universe, there is a comic book series named Ben 10. In that universe the creators of the comic are either approached by Cartoon Network or put forward the idea themselves to the network. And so the comic receives an cartoon adaptation. And as a tip of the hat to the fact it's a comic, a couple of episodes feature a comic book at its start and end (like how Superman features a comic opening at the start of his film). And that's the real reason why we see the comic. However, to our universe it doesn't make sense because Ben 10 started life in our universe as a cartoon rather than comic.
 * Alternate theory: Ben 10 really did started out as comic in Real Life. However, the comic is very obscure, which is why we never heard of it before.
 * well yes, Dial H for Hero is pretty obscure

Future Ben (from Ben 10,000) was responsible for blowing out his timeline
At the end of that episode, Future Ben gives Present Day Ben a cake. This caused the timeline to diverge. In the original timeline, Ben had no cake for grandpa. In this new timeline, it is the mere presence of a cake for grandpa that causes the timeline to diverge and lead to Alien Force. Hence, the Butterfly Effect.

Or if you want you could put the blame on Future Gwen for taking them out of time in the first place.
 * Makes sense, especially since Future Ben didn't seem to remember the events of that day.

The master code when used to go Ditto or Echo-Echo can result in an army of all the Aliens
Ditto and Echo-Echo can make copys of themselves + the Master Code allows instant tranformations = Omnitrix Army
 * Ditto does not work that way. What happens to one happens to all; It could only potentially work with Echo-Echo.
 * As of the 2nd episode of Ultimate Alien, this is canon with Echo Echo. Unfortunately, Ben's turned back into an Idiot Hero, and he gets in his own way when he uses multiple aliens.
 * It could be that (perhaps due to the acknowledged flaws in Albedo's workmanship in the Ultimatrix, which would also explain the split personality that never manifests when Echo Echo is used normally), Ben's brainpower was split equally between the copies. Since even at his best he's no genius to begin with, each of Ben's bodies being at 1/3 the usual intellect would explain a lot about that fight.

Synaptak was an unused design for Grey Matter
Think about it. One power Ben was missing in the first series was psychic powers. Synaptak has psychic powers and a high intellect. So, chances are, Mr. Brain-in-a-jar was in a similar situation as some unused Upchuck designs. Number one became the villain Sploot in Ken 10, number 2 became Spitter, number 5 became the villain Gullet in Ken 10, and number 9 went under a big time modification to become Arcticguana. Besides, the creators probably thought it would be funny to have a tiny alien not suited for combat, so Synaptak got ditched, which is a pity.

Ben is a Furry
In Perfect Day, he turns Gwen into a rat so they will not catch on to him

Sumo Slammers is Samurai Jack
A show featuring a japanese man against an evil shapeshifter? It's gotta be

The Live Action Adaptation was a nightmare of Ben's.
The other plot in the movie was about him adjusting back to a normal life. The fear of going back to being a normal loser when summer ends manifested itself in a nightmare. Think about it, it makes perfect sense. The underdeveloped villain,the continuity errors,everything!

The Ben 10,000 timeline IS an alternate timeline from Alien Force and Ultimate Alien, but...

 * It's the same timeline as the original series. How is this possible? Well, Alien Force and Ultimate Alien are Alternate Timelines to the original series/10K; in the OS/10K timeline, Vilgax is an irredeemable Complete Monster from the Null Void Frontier who, in all likelihood, almost drove his own people to extinction, which explains why Myaxx fears him. Not only that, but the Plumbers ARE merely an Earth-based MIB. Oh, and Gwen's powers come from magic; she isn't a half-Anodyte hybrid. Finally, Kevin never redeems himself and is inherently a Sociopath; the reason for all the Character Derailment, Continuity Snarls and such in AF/UA is simply because they're not the same timeline as the original series. It makes it a hell of a lot easier to enjoy both the original series and its "sequels," even though the sequel series DO have writing of a slightly lower quality and the animation doesn't look as nice due to the dimmer palates and less aesthetically-pleasing art designs. Also, some of the aliens from the AF timeline ARE eventually made available to Ben in the OS/10K timeline; to be specific, one of them would be Rath.

Sequel Series aliens will one-day undergo a redesign that makes them seem "first-series".
As in, more apparent clothing and having the Omnitrix somewhere other than the chest.

Professor Paradox is a time lord
he was a time lord that came to earth became human using the chameleon arch and worked on a project to create another version of the untempered schism but when it was finished he fell into it, the pocket watch is his chameleon arch