Pokémon Colosseum/WMG

This takes place in The Matrix.
The people refer to the higher-ups as "admins". This is normally used in online gaming, not in organizations.

And Peons are Agent Smiths.
 * Then all of Pokemon takes place in the Matrix, since pretty much all the higher ups in every evil team save Plasma are called Admins.

Rui and Michael are related.
Seriously I can't be the only one who thought this. They both have red hair and have something to do with Shadow Pokemon. Also it would kinda make sense. After the events of Colosseum, Rui is so distraught, and so determined to ensure that Cipher to never makes Shadow Pokemon again, that she goes to her mother/aunt (Michael's mother) and asks her to help people prevent this from ever happening again. It would be very easy to develop the Aura Reader if they had a biological example right in front of them.
 * Then wouldn't that mean that Michael is also related to Eagun and Belluh, who both are clearly unfamiliar with him when they first meet? Eagun could be excused as simply being scatter-brained, but Belluh seems to be the sensible and rational one, who could easily remember a grandson or grand-nephew or whatever relation they might be.
 * Original poster here. I see what you mean. Well, it could be that they just never met him, as Michael doesn't seem to recognize them either. Still, that is a good point you bring up.

Wes and Rui are Misty's parents.
Rui sorta looks like Misty. As for why her sisters look nothing like them... it's anime. Relatives don't always resemble each other. Or maybe they're adopted.
 * This whole WMG is based off similar looks, and then you say that similar looks don't matter.
 * I seem to recall Misty saying that she was born and raised in Cerulean City. Orre =/= Cerulean, and there's not really a reason that the two would just uproot themselves and move over to the distant land called Kanto just to be able to raise their daughter somewhere else.
 * It's quite possible / likely that Rui is an Expy of Misty (they're both red-haired tsunderes, etc.), but them being actually related is fairly unlikely given that game and anime continuities are separate.

Wes helped capture most of the future Shadow Pokemon.
The partnership between Snagem and Cipher worked like this: Snagem steals and captures Pokemon, and delivers them to Cipher to convert them into Shadow Pokemon. Wes is obviously a Badass, seems to be the most competent of Snagem, and Rui calls him a snagging expert. It's quite possible that Wes helped capture a lot of the Pokemon in the first place, including the legendaries. The realization of how Shadow Pokemon work and the fact that he was mostly responsible set off his Heel Face Turn.

Wes spent the time period in between Colosseum and XD working to renew Orre for wild Pokemon.
Because.

The Skarmory that is seen at the beginning at the game is the same Skarmory that Gonzap later uses in the battle against Wes.
Gonzap likely captured it at some point after Wes blows up the headquarters, and had it turned into a Shadow Pokemon.
 * I always thought that it was already his. This works too, though.

The Pokemon Center nurses are actually robots.
When Wes is in Pyrite Building, he can heal his Pokemon like at a Pokemon Center, except he must do it himself due to the lack of nurses. The machine says what all the nurses always say. Nothing ever says the nurses are the ones speaking...
 * Which leads me to:

The Pokemon Center nurses are silent.
The above theory explains this one.

Eagun is Ash.
Let's see... Eagun's very first Pokemon was Pikachu, he's seen a Ho-oh, and was once one of the best trainers in Orre, if not the world. Yep, sounds like Ash.
 * Jossed for a couple of reasons: The games and anime are separate continuity and in Colosseum Eagun says that he's never "seen a Ho-oh that close before."

Eagun is a Recursive Adaptation of Ash.
Ash is the anime-counterpart of the game character Red, and while they share similarities, they're not the same character: Red, for one, seems more like the strong, silent type than energetic little Ash. Eagun is the game-canon's way of taking Ash's hyperactive personality and love for Pikachu and making it its own. Why is he an old man? Rule of Funny.

Orre is what happens when a protagonist fails.
It's not naturally a desert (under the premise of the guess), and Olympus Mons could do something like that easily (Groudon nearly did, in Ruby).

Reshiram and Zekrom are what happened to Orre.
Unova's right next door if the Pokéworld geography is at all similar to ours, and they raged across half the continent during their big battle. Maybe Orre was a main battleground.

Michael has a Death Note.
In XD, whenever you beat a Rider, he will clench to where his heart is and fall backward. Perhaps it was a Heart Attack by nothing more than a certain Trainer's Death Note.
 * Boy, it must be a pretty lame one then, since you can, y'know, talk to them immediately after.
 * Maybe he has a Death Eraser, like the one from that one Death Note omake thing. He's just a total sadist that scares the hell out of them by killing them and bringing them back to life just for shits and giggles.

Colosseum/XD take place in the far future compared to the main series.
There's the possible evidence that Eagun is older Ash, of course. There's the FLYING. FUCKING. CARS. (Or just the tech in general -- it seems a lot more advanced than any other gen. (Silph Co. seems almost to par with Orre, but even THEY didn't have FLYING. CARS.)) There's also the lack of any Pokemon League that may have deteriorated over time, but that could always just be physical isolation. In a similar vein, the lack of wild Pokemon (at least in Colosseum) hints that Orre wasn't always a desert, because TONS of animals live in the desert IRL.
 * Hoenn had a desert full of Pokemon (mostly Sandshrew, Cacnea, and Trapinch), so it isn't as if there aren't any Pokemon who can survive there.
 * The Battle Frontier Island off the coast of Sinnoh has a desert, too. As does Unova.

Orre is only crime ridden because of the current government.
Note the only presence of law enforcement is in Pyrite (checking a map of Arizona puts it in Maricopa County, known for its tough Sheriff). Arizona at the time of the game's release had a noticeably incompetent Governor. Note that aside from Kanto, the villain teams are all opposed by the regions' Champions; the reason Battlus isn't doing anything about Cipher is that the current government is holding him back.
 * That or the huge distances between any kind of civilization, so far that the protagonist can't even be expected to walk...

Gorigan is the Engineer's brother or cousin.
Tell me this guy doesn't look like this guy.

A future main game generation (VI or beyond, since it's too late for V) could have Cipher as a concealed threat.
Do you honestly think a group with some unrepentant Complete Monsters in its cabinet will give up on its profane ambitions after two defeats like Team Rocket? It's obvious they have enough resources for another go, even after XD, and more than enough intent to carry on. Here's all the evidence to support this theory.
 * First off, Cipher is the kind of group to run its operations behind the scenes. It's kind of a stretch for most people to think of Es Cade as being Big Bad Evice without [A] being uncomfortably paranoid or [B] having read about it elsewhere, and the same could be applied to Mr. Verich and his "bodyguards". They have experience in the field, and their personnel training methods border on Paranoia Fuel, which means law enforcement would be hard pressed to go after them without a lot of evidence (think of Sherles and Johnson as "practice" if you would, though fooling a total moron like Johnson doesn't take much). Hiring out a legitimate group as a proxy or, perhaps, Running Both Sides of a "government vs criminals" conflict would serve as an added cover to keep their hands proverbially clean.
 * Second, Wes left Orre for parts unknown after Colosseum and was never heard from again, and Arceus knows what Michael will be doing. That leaves Sherles, Johnson, and some makeshift vigilante force to keep two generations of Cipher behind bars; Sherles and Johnson couldn't even keep Miror B.'s goons locked up for more than a day, Team Snagem is more about "king of the hill" than keeping the peace, and not even a thousand Xatu in a thousand years can reliably predict how any vigilante force would remain motivated or competent against such a threat. It's not a matter of if, but when, Cipher will get out of jail, and it's hard to predict whether Greevil's surrender after XD was genuine or just an act to plot an inevitable return.
 * Third, Ardos has stated with the subtlety of a Rampardos that he intends to rebuild Cipher even after the group has broken apart (see "Sequel Hook" on the main page for more information). How do you know he hasn't backed up anything vital or looked up viable contacts prior to the big arrest? With lunatics like Ghetsis and the Shadow Triad running loose, odds are he's going to find some kind of audience for his ambitions before he dies in his eight-by-eight. The only folks who are paid to keep this shit under control are Sherles and Johnson... oh, wait.
 * Finally, and this is the most depressing part, the rest of the world could not give a crispy shit about Orre! There is not one instance the region is referenced BY NAME in any other Pokemon game, even amongst the prestigious Ranger Corps! Black and White has yet to hit US shelves, so it's hard to know if they buck this trend, but if not, this troper is more than ready to believe Cipher is more than capable of utilizing this lack of knowledge for their own ends. Remember the old adage "Evil wins when good men do nothing?" How can you do jack shit when you don't know what to do jack shit about?
 * A Plasma Grunt says they realized Team Rocket and Galactic failed because they were too obvious about their work. Cipher seems like a dream team for them.
 * Cipher doesn't get mentioned in Black and White. Orre is just across the continent from Unova. N's gonna have his work cut out for him...
 * Has everyone forgotten that the Orre games are spinoffs? Yes, they can trade with the other third gen games, but that was just for Pokédex completion. The main series isn't really obligated to mention spinoffs anywhere.
 * Yeah, except the latest wave of spinoffs (Pokepark, Rumble, Nobunaga's Ambition) are completely isolated from the main series, so your argument doesn't hold water. Even the Ranger subseries has continuity within the anime and mangas. Colosseum and XD NEVER had that luxury.
 * I thought we were talking about the game continuity, not the anime or manga. Yes, even Mystery Dungeon also had anime specials, but the anime and game canons are clearly separate, and when did the main games ever mention Mystery Dungeon, Ranger, Rumble, or anything else? And if they don't mention anything else, then I see no reason why they should mention Colosseum or XD. More importantly, though, the trading is the only connection to the main series games, and that was only done so we could have 100% Completion in the Pokédex. The story lines are still completely unrelated.

Wes will be a Bonus Boss in a future game.
"Left for parts unknown"? While just an excuse to not have him crush Cipher in XD, seems interesting. My guess is he will be in the Contest of Champions Cynthia suggests in Black and White when it comes about.

California has experienced a Deus Ex style sinking.
Hence the presence of an ocean far thicker than the Colorado River, complete with port.

Lovrina is related to Ein somehow.
She's either his younger sister, daughter, or just his pupil, but she got her scientific talent from him.
 * Maybe a relative of Venus that he trained?
 * Bonus points if she's related to both Ein and Venus (their daughter? A shared niece or cousin, maybe?), as she acts quite a bit like both of them.

The three uncaptured and unrepentant villains will team up.
Ardos, Ghetsis and his Shadow Triad, and Cyrus will team up. A match made in... I'd say hell, but it's often interpreted as exactly what Cyrus wants. As for why Cyrus (destroy the world and remake it without emotion) will team up with the other two/five, to quote Bulbapedia, "Shadow Pokémon are created through an undisclosed process that removes the Pokémon's emotions, turning it into a soulless fighting machine", and Ein refers to the process as "shutting the door to their hearts"; perhaps he would like to use the process on humans. All 3 are easily sick enough to do it. Bonus sicko points if he does it (and Ardos goes along with it) on Eldes, who tries to stop him. Given we have a Wii game coming out, rumored to be an XD-like game, it may not need to wait till next gen.

Nascour really WAS Cipher's leader.
Nascour doesn't seem like the type to truly be loyal to Evice or Greevil. He seems like he'd be a Dragon With an Agenda, and was actually the guy who ran Cipher's plans and kept it working like a well-oiled machine, while Evice and Greevil were the guys who provided the finances for Cipher and reaped most of the rewards of its activities. Naturally, this pissed Nascour off, so in between the games, he's ascended by killing Evice and Greevil. And now, he's allied with Ghetsis and Cyrus, who execute other parts of the plan, and Giovanni, who provides the finances.

Colo is the chronologically earliest game in the series.
DPPHGSS takes place three years after RSFRLGE. Bonsly is referred to as a new species five years after Colo in XD.
 * Maybe. The "new species" thing is referring to it being introduced in Generation IV, not to it being newly discovered. As a sidenote to that, the only confirmed part about the timeline is that three years pass between RBY/FRLG and GSC/DPP/HGSS; there's no proof for when RSE, Colosseum, or XD take place.

Shadow Pokemon handed out by Cipher had their Poke Balls tampered with.
The only way Shadow Pokemon can be purified seems to be with the main character, despite non-Cipher trainers having them. They would've been handed a Poke Ball with the Pokemon in it, by Cipher who were handing them out. So the balls were tampered with to make it so the Shadow Pokemon couldn't be purified. When you snag one, it gets put in a new Pokéball that wasn't messed with and thus is purifiable.

Michael is actually Wes and Rui's son.
Wes and Rui married and retired as trainers, but noticed suspicious activity and feared that Team Snagem was not really finished. With the conception of their first child, they made an agreement. They are confident that this child will want to oppose Team Snagem and be a great Pokemon Trainer. They also plan to leave the region to live in peace somewhere and wish to know that Orre will be safe in the future. The child was born and named Michael. When the boy was a number of months old, Wes and Rui went back in time. First of all, certain Pokemon have been known to transcend time. Also, with the technology displayed in the game, time travel doesn’t seem like that much of a stretch. Anyway, they gave the boy to Lily and her husband to raise, along with an Eevee egg, the parent of which is ether Wes's Espeon or Umbreon (Or possibly both, should they be of the opposite gender). Whats more, they ask the surrogate parents to not let anyone know that Michael is their child, as to protect him from Team Snagem until he is ready. Also, the machine that Michael has doesn’t really work, he has inherited his mother's ability to sense Shadow Pokemon. The machine is just another step to keep him or anyone else from discovering that he is Wes and Rui's son, by hiding this ability.

This explains a number of things. First, how Michael looks like Rui rather then Lily or Jovi. Also, how he received an Eevee that was from his father, when Eevee is understood to be quite a rare Pokemon. It also explains Michael's serious demeanor, drive to oppose Team Snagem, and what seems to be a natural talent for capturing and purifying Shadow Pokemon, all of which he has gotten from Wes. It also explains why, even after losing her husband, Lily would allow her ten-year-old son to go off on his own to fight an evil organization. Because he was not really her child, and it's what his real parents wanted of him.
 * He doesn't look four years old.

Wes knows how to make Poke Balls.
You know the infinite Poke Ball glitch in Colosseum? I say it's not a glitch. Our hero just knows how to make Poke Balls himself, as long as he has at least a couple of templates.

Eevee are native to Orre.
In the games, Eevee are never obtained in the wild, only as gifts; the only place you can actually catch an Eevee yourself is Mr. Backlot's Garden, and it's known that he imports his Pokémon. Henceforth it can be hypothesized that Eevee are not native to any of the main game regions, and perhaps have all but died out in the wild, surviving only in captivity. Meanwhile, Orre is a region where wild Pokémon in general are a rarity, and in both games, you start out with Eeveelutions (an Espeon and an Umbreon in Colosseum and an unevolved Eevee that you are soon given the choice to evolve into any of its five then-existing evolutions in XD: Gale of Darkness). Perhaps wild Eevee used to live in Orre, and the reason there are no more wild Eevee is because Orre is no longer fit for wild Pokémon to live in.
 * Maybe they're native to the entire Poke-America continent? Pokémon Black 2 and White 2 have Eevee added to the Unova 'dex.

The Peons aren't really clinging to the ceilings. They're using Portal technology!
Shoot a blue portal on the ceiling. Shoot an orange one in your guard post room. Observe from the orange portal if anyone passes through. If so, jump through and surprise the living bejeezus out of them! This would also explain how a mook is able to enter an elevator after you get on (though it would not explain how a portal stays open on a moving surface...)
 * In Portal 2 there's an instance where you can place portals on two moving panels. Make the elevator tops out of that stuff, and tah-dah!

Bill is Micheal's father.
Incredibly talented inventor, gave a loved one an Eevee. Apparently poor Bill is dead now.

A history of Orre, and why it's a miserable place.
Centuries ago, the region of Orre was little more than a desert. A group of immigrants, originating from Pokepan, settled on the land. They tried their very best to survive the harsh terrain, but it was all for nothing. However, a friendly Celebi took pity upon them. It decided to allow the region to flourish. For most of its history, Orre was a happy place. But the citizens began to covet the great Celebi's power. They thought that to ensure their society became a total utopia, Celebi must be captured.

This was an abject failure. Celebi, infuriated with the betrayal, took back the gift it had given. Wars broke out, and Celebi ended up fatally wounded. It was at that moment the people realised the error of their ways. They begged Celebi for help, and tried to save it. Celebi used what remained of its power to keep the region alive, as best as it could. It told them that it was with child, and a new Celebi would look after the region. Only when they had proven themselves worthy, would it restore their lands.

While most citizens were happy to earn their freedom, a few were infuriated. They claimed that Orre should not be punished for trying to capture Celebi, since it was misguided instead of evil. That group was determined to harness Pokemon's innate power, and restore the region. But the darkness in their hearts had shown. Over time, they would lose sight of their goal, and begin to work only for themselves. They were known as Team Cipher. Their leader, Greevil, failed to realise this. Only when a trainer defeated him, did he realise he was working for no-one but himself.

Cipher offed Wes sometime between Colosseum and XD.
Really want to be wrong here, but it would explain his absence during the sequel...

Charon invented Shadow Pokémon.
In Pokémon Diamond and Pearl Adventure, he uses very similar technology to enslave armies of Pokémon. We know from HGSS that he's basically a free agent, working for whoever wants his particular brand of mad science...
 * In another manga, a bomb, planted by Galactic, unleashes a Hate Plague upon the Pokemon near Lake Valor. Pearl was there and caught one of these, and he usually has to put his opponent between himself and that Pokemon in order to get it to attack the proper target. Attacking humans directly. Sound familiar?
 * But don't the Ein Files in Colosseum specifically state that Ein made Shadow Pokemon?
 * Of course Ein would say that he invented them, but it doesn't mean he couldn't have stolen the research from someone else, right?

We will see a new Cipher plot in a future game, and Shadow Darkrai will be involved.
The game will provide Darkrai's Start of Darkness, explaining how he went from a fairly decent, even heroic Pokemon with an unfortunate power he can't control to Pokémon Mystery Dungeon: Explorers' Complete Monster. After a long time of secluding himself alone on a little island to avoid his powers accidentally hurting innocents, he was Mind Raped into a Shadow Pokemon and never truly recovered until his memory wipe at the end of Explorers.
 * Or, the original Darkrai was behind this all along, and the good Darkrai in the Anime and games are just wayward escapees from the Dream World, where he was sealed away. Naturally, being a living nightmare, Darkrai's power'd end up creating clones of himself. Hey, if Legendaries like Dialga, Palkia and Giratina can come from the Dream World (Explaining their Hidden Abilities), so can Darkrai.

Nascour and Evice are psychics.
It's why Nascour's hair seems to have a life of its own and why Evice floats when he's pissed off. This is also how Dakim survived jumping off the edge of Mt. Battle -- one of them (probably Nascour) was waiting around and teleported him.

In the sequel, Garchomp and Hydreigon will be Shadow Pokemon.
The previous games had all the pseudo legendaries as Shadow Pokemon.
 * Shadow Hydreigon would provide some excellent Nightmare Fuel, given how scary it is already in Black and White...

Ghetsis is an agent, or at the very least in league with Team Cipher.
For obvious reasons. His Hydreigon also has perfect IVs and EVs, like most shadow pokemon before purification, and he doesn't strike this troper as the sort to train his pokemon lovingly. He probably knows them even more thoroughly then we think. Possible sequel to XD? Please?
 * Getting rid of all normal Pokémon would allow shadow Pokémon to dominate the people even more.

Adding to the previous Wild Mass Guessing, Ghetsis is helping Team Cipher spread its influence to other regions.
While Team Cipher can easily thrive in a place like Orre, an economic power like Unova could prove a pretty big hassle for them. Enter Ghetsis. The reason why he decided to conquer Unova by getting people to relinquish their Pokemon isn't just that it's going to be easy method of power, but that it'll make Cipher's invasion all the more easier. The reason why there's no Shadow Pokemon is due to Pragmatic Villainy: Ghetsis has done all he can to keep a Villain With Good Publicity angle. If he shows up with a Shadow Pokemon, it's going to turn some heads. Many of the technological villainy Team Plasma has done(hacking into the PC, creating Genesect) is an attempt to find alternative methods to the raw power of Shadow Pokemon. As for Reshiram/Zekrom, it may be a sign that Ghetsis is an ally to Cipher instead of a member. Ghetsis is the kind of guy who'd want to be in charge of things, so he might've kept these Pokemon to fight off Cipher and/or conquer them.

The white mark on Wes's face is a scar, and a Mark of Shame.
Emphasis on Mark of Shame. He got the marking during the process of betraying Team Snagem, or an earlier villainous team whose actions led to him becoming a serial Team saboteur. The mark may actually be as regular as it is because it's a tattoo to hide a scar.

"Parts unknown" is "any place that an evil Team of Pokemon gangsters is causing trouble".
See above. Wes is a serial saboteur of evil Teams. This especially crosses over with the spirit of the guess above that we'll see him again, though not the letter, in that he may be an ally (or at least the enemy of the PC's enemy) rather than a Bonus Boss.
 * He works for, with, or is the boss of Looker.

The white mark on Wes's face is a burn scar, and a Mark of Shame.
After the first time a person leaves their metallic visor on their bike in the desert sun, picks it up with a gloved hand, and tries to put it on without leaving it in the shade for a while, that person never makes that mistake again.

Wes' stripe is a tattoo.
And he got it solely in an attempt to look more Badass. Sure, it's a pretty simple one, but from cheek-to-cheek across the bridge of the nose? Ow.

The white mark on Wes's face is zinc oxide.
It doesn't work very well if you don't rub it all over the exposed skin of your face, but he might have had regular sunscreen/suntan lotion on the rest of his face and used the zinc oxide for a fashion statement.

The white mark on Wes's face is ice cream.
Nobody who realized it wasn't intentional was willing to risk feeling awkward about telling him he has a huge streak of ice cream across his nose. Wes ate an ice cream cone and accidentally wiped some from his sleeve to his face shortly before defecting in the prologue, went through the game (a fairly short length of time) with it on his face, then shortly after the game noticed it while washing his face in a club for rich people with one of the few intact, full-sized mirrors available in Orre. He didn't notice when walking by the shiny water in places like Phenac City because he's not a narcissist, sheesh, you think everyone does that? He didn't see it in his rear view mirror because he uses those to watch behind him, not to look at his face while driving. Ice cream is sticky, but then again, so is quickly-drying (and therefore non-running) sweat, and his peripheral vision isn't very good (what with his eyes dilate from sunlight all the time), so he doesn't notice that part of his always-blurry nose is lighter than (but about as shiny as) usual.

Dakim does a Heel Face Turn and becomes Alder.
Seriously, look at them. They're both huge. They both have crazy red hair in almost the exact same style. They both wear mostly white and have necklaces of Poke Balls. Also, Dakim is able to leap off Mount Battle and survive, and in Black and White, Alder leaps off a freakin' cliff when the stairs are right there and isn't even hurt. Geography-wise, Unova shouldn't be far away, so who's to say after Cipher collapsed the first time Dakim didn't hop across to Unova and turn over a new leaf? It's not like Orre's flimsy authorities would be able to stop him. His full name could be Dakim Alder, or Alder Dakim, or maybe Alder's just a name he made up so no one could track him. A name like Alder wouldn't be out of place in Orre.

Additionally, perhaps the reason he's taken Marshal under his wing is because Marshal's former Blood Knight status hits Dakim/Alder a little too close to home, so he's trying to get him out of it. He'd know how to get him out of it, since he's been through the same thing.

(There may be a similar theory over on the Black and White WMG page, but I haven't checked).
 * You'd think that would be the kind of thing Ghetsis would bring up when mocking Alder about his past.
 * Perhaps he just isn't aware of it.
 * Ghetsis's plan seems to be more about guilt-tripping people about the Pokémon themselves, rather than what kind of trainers the people might be. Note he doesn't bring up much about Alder's past except for the dead Pokémon.

Ho-oh's reason for showing up at the end of the first game.
Because it's pissed off at Cipher for turning its friends/servants (the legendary beast trio) into Shadow Pokemon.

Why they chose to make Lugia into XD001...
Somewhat related to the idea above: Greevil already had the original legendary bird trio. Lugia is the leader of the bird trio, and thus, Cipher captured it and turned it into a Shadow Pokémon to keep it from attacking them like Ho-oh had done before.

Orre is Cyre/The Mournlands
Look at the Colosseum map and see how many individual regions border it. Granted, XD shows more of Orre is to the west. Having been beaten down by the collective military force of multiple nations would be a reason for its wasteland stats.

Some of the intended Shadow Pokemon from Colosseum were released into the wild by XD.
Hence the Pokespots.

Michael was lied to about the time between Colosseum and XD.
Wes told everyone from ONBS to pretend it was only five years so Michael wouldn't think of Cipher as weaker than before, and so not to let him know that the new Snag Machine took years to develop and is still a prototype. This is supported by one fact - how could Michael not remember something that happened when he was eight? Also makes the "Michael and Jovi are Wes and/or Rui's children" theory a tad more possible.

When They Eventually Make a New Game, Miror B. Will return
And he will have Bouffalant. Because that species was made for him. Hopefully they'll have pokeball afros too.

Team Cipher has used the Shadow Pokemon process on humans.
It would be perfectly in their character, so why not? It could be very possible that some of the Cipher heads were the result of this.
 * Most likely, it was Dakim. Non-voluntary, of course.

Orre is undergoing development into a thriving region, and the next Orre game will have a full League
In Pokemon Colosseum, the entire area, with the exception of Agate Village, is inhospitable to Pokemon - well beyond the sort of conditions found in regular deserts. However, by Pokemon XD, the area has grown somewhat less inhospitable, resulting in the appearance of Pokespots, and the rudimentary components of a fill Pokemon League are in place - there is a "Pre-Gym" in Phenac City, and there is a location with an ersatz Elite Four. There is even a Pokemon Professor who has apparently moved to the region, in part to study Shadow Pokemon purification, but, I assert, also in part to study the region's changing Pokeclimate and the development of pokemon ecosystems.

In the next title set in Orre, set 10 years after the previous title, many parts of the map will be lush to one degree or another, and it will actually be possible to walk from one location to another. Furthermore, true wild battles will be possible, as many more pokemon will have moved into the region. Not only that, but a full gym system will be in the process of being put into place, with some of the gyms only barely having been completed by the time that the player arrives, but all eight gyms will be operational, and will give out badges, required to challenge the Elite Four.

Professor Krane will give out a Starter Pokemon, but it won't be one of the regular starter lines. Furthermore, the player will immediately be shown how to capture wild pokemon, and the wild pokemon caught will actually be the player's second pokemon immediately. Agate Village will have a Moss Rock near it, while an Ice Rock will be found in an icy cave hidden a short way up Mt Battle. Mt Battle itself will hold, at its peak, either Michael or Wes (likely the latter), who will give out their game's Johto Bird Legendary (Ho-Oh or Lugia, respectively) if you can defeat them. A number of starter pokemon from other titles will be found in the wild, too, likely including the Johto starters (after all, they've shown up in both games - shadow pokemon of the middle stage evolution in Colosseum, regular first stage forms in XD).

It may even turn out that Professor Oak makes an appearance in Orre, in the next title.

To up the ante, Team Cipher will obtain a Shadow Celebi.
To be precise, the very Celebi from Agate Village. Cipher will have had enough of purification, and so try to stomp it out at its source. They do despise goodness, after all. Plus there's the fact that it would allow people to finally get Celebi without event, much like Ho-oh and Lugia in the Colosseum and XD games.

Mirror B left Team Cipher because of work ethics.
Mirror B, while he worked for what is essentially Team Rocket's eviler twin, never seemed to be on the same level of evil as an organization that mentally tortures Pokemon into living weapons. He seemed more focused and dancing, plus he treated his Ludicolo army as living things-considering his love of using them in battle and disco. I assume that either he was fired because he didn't take his job seriously, or Mirror B didn't have the stomach for taking the job seriously(aka making Shadow Pokemon instead of just selling/training him.)