X-Men: Evolution/WMG

Aliens are involved in the Evolution universe, but not directly seen
The Shi'ar and the Celestials would be the most likely candidates. They're never at the forefront, but their influence is still felt. For example:
 * The plane crash the killed Scott and Alex's parents was caused by the Shi'ar, just like in the comics. Scott's dad is either living it up as a space pirate named "Corsair", or hidden in quarantine because of his knowledge of alien involvement in Earth.
 * The technology in Apocalypse's tomb is the product of a crashed Celestial spaceship. Had the series continued past season 3, the team would have explored the technology's alien origins.
 * Area 51, where some of the team was held captive at the end of season 2, is also home to some scavenged Shi'ar technology that the government has been studying since some Shi'ar crashed on Earth back in the 1960s. Bolivar Trask's Sentinels use weapons reverse-engineered from the crash sites.
 * Magneto's base in Asteroid M is actually an abandoned Celestial enclave. His power-enhancing machine is reverse-engineered from technology he found inside it. Ditto for the machine that keeps him young.
 * Jean will discover her potential as the Phoenix (as seen in Professor X's vision of the future) when Lilandra and co. visit Earth to investigate what happened to the lost Shi'ar that went missing decades before.

Mystique will have her vengeance on her kids for shunning her after everything she's done for them.
As her frown suggests in the final episode. She's not gonna let it go.
 * "Everything She's Done For Them" includes allowing a genocidal Knight Templar to experiment on them, abandoning them, lying to them, sending her goon squad to beat the shit out of them and their friends, and attempting to outright murder one of those friends.
 * Yet, she's still angry at them for shunning her.
 * Because she's a PSYCHO.

Deadpool exists in Evo
While its often said that Omega Red said 'Wraith & Mavorick' he actually said Wade as you can tell with a distinct 'D' sound after the 'wray' sound, his accent may mix it up, but you can clearly tell what he really said. Wade is clearly Deadpool, who clearly exsists in the Evo-universe, so if Evolution had a season 5 Deadpool would appear, as seen by the large amounts of Fanfiction with Wade in.
 * He might exist in Evo, But Omega clearly mentioned Wraith and Maverick.
 * I heard a 'D', its either his accent is making him mispronounce the 'ith' sound as a 'De' sound, or its Deadpool he's talking about.

Logan is a stripper
Just try & deny it.

Kurt's foster parents are Rogue's biological parents
Wouldn't it be hilarious?
 * Mystique kidnapped Rogue at birth and dropped her off with Destiny due to Rogue's powers. Kurt's parents adopted him after Mystique abandoned him to "replace" their stolen daughter. Ta-da.

Magneto's Power Enhancer Machine Didn't Actually use the Crystals of Cytorak.
Why would the "Ultimate" version of Mystique's powers make her default form a blue female body builder? The whole crystal thing was nonsense to disguise the fact that all Magneto's machine really did was pump people full of steroids and brainwash them. The X Gene is actually physiological, so steroids could enhance it's effects, but enhancing Mystique's, Havok's or Cyclop's powers does not logically lead to their Post-Enhancement physiques. More logical physical alterations are for Mystique's body to become less humanoid and more amorphous, Havok to become more akin to the Human Torch, and Cyclops to become more of an energy being. There's also the fact that canonically to the comic universe the crystals are magic (and the source of Juggernaut's powers), not radioactive.
 * I assumed that the Gem worked the same way as the Super Soldier formula, IE, puts them to their physical prime, and for mutants, this includes their powers. The effct of the Rebirth/super soldier machine did the same thing the gem did to Magneto. Your explanation works too, but this is how I saw it.

Tabitha's personality, ie, boundary issues, is primarily a result of being raised by a semi abusive, petty criminal father.
Her father has no problem using his daughter to steal money, and has no problem stealing money in the first place, basically living with a "everything is mine" mentality. Tabitha is a much better person, not believing theft (from people) to be acceptable, but borrows without prior permission and has little problem vandalizing machines for money/drinks/etc. But it's still a result of being brought up by a man who uses everything and everyone. She is used to, if not ok with, taking what she wants, so long as no one is harmed/she gives it back, and flirts with pretty much every guy she sees, because having shown interest could always come in handy later getting them to do something for her.
 * Isn't that cannon? Isn't it suposed to be that since she had such a douchy father she was so messed up and acted like that?

Lance didn't go through character Derailment in Season 2, it was an act
Lance changed in season two, no denying it, he had a complete change in personality. This is the definition of Character Derailment. While he returned to being a jerk, he later showed at least some sense of right and wrong. However, It wasn't character derailment. Look at the 'good personality, look at the first episode it happened and the first episode he reverted. In the first, he starts of only acting like a nice guy in front of Kitty and was clearly still villainous and possibly sociopathic. tThe episodes afterwords he only demonstraights nicenes as most of his appearences involve Kitty somewhere, but when Kitty isn't around, he acts insulting and provoking. When he reverts, Kitty tells him simply "This is the real you isn't it? You're nothing but a hood!". He was never Nice, it was an act. However, Becoming the Mask falls into place, and during his time as pretending to be nice he developed some more positive aspects, so while still Villainous, even a violent and villainous angry youth with shak'em powers has standards. While he did like Kitty, he was still an agressive mutant who only pretended to act like that. Bare in mind, I used to hate Avalanche because of his Character Derailment, now, I see him as a Magneto like mutant, who after pretending for a while to be a nice guy, actually developed a mix of different morals, in fact, this perspective on him actually makes him now one of my favourite characters. Seriously, I hated him when it seemed the writers failed, but now, it seems like he's a much more complex character and I think its awesome. It pretty much blew my mind when I realized he just became one of my favourite characters, possibly my favourite B-hooder. Amazing what happens to your opinion when you try to look at it from someone else's point of view.

Gambit was with Sinister when the fight with Apocalypse was going down.

 * Granted, there's no evidence that his powers were going haywire, but it'd be ultradramatic.
 * A fanfiction I read a few days ago actually said that was what happened, something to do with his eyes, and that he was assigned to spy on Magneto fo him.

Had the series continued, Legion would have reappeared as the new Big Bad
. And his first act would have been to strike at Xavier by attacking the Xavier Institute and/or possibly telepathically manipulating the X-Men into doing his bidding, or something similar.

Mister Sinister would have became a major player had the series continued.
Similar to the previous one, Sinister would have came to manipulate the post-Apocalypse situation to his advantage, likely involving lots of Mind Rape and such.

The Brotherhood did NOT have a Heel Face Turn at the end of the series
As noted just about everywhere, the Brotherhood were seen to join SHIELD at the end of the series. But, one thing that's always bugged me about that, as I've noted on other pages, was Xavier, in his comentary on this scene, seemed, well, less than thrilled about them. He basically said that some people never change, and his tone sounds like he's disapointed. As well as that, the Brotherhood's future designs are, well, not exactly the most heroic or SHIELD issue looking duds. For one, most of them have what look like Slasher Smiles, their clothes look outright villainous, and Blob and Toad still look like their Evil Is Ugly appearences, only older. So, this has lead me to believe that the Brotherhood didn't become good. I have two theories why: Either A) They didn't join SHIELD, the background was either a mistake or not meant to mean they join SHIELD. Or B) They joined SHIELD, but like the comics, it didn't stay as heroic as it should have been, either being corrupted or taken over. Massivly over used plot in comics is SHIELD being infiltrated and turned evil. I don't remember where, but one source said that in the end they joined/formed Freedom Force, an Evil!Goverment sanctioned team from the comics, which would either be option B, or its own, new option, Option C.
 * They joined SHIELD. Word of God says so. The Brotherhood were not evil unless someone was manipulating them. But they also didn't want to be heroes or X-Men. So SHIELD fitted them. Like the Runaways, they existed outside of both Xavier and Magneto's vision of what mutants should be. So it is easy to see why Xavier was disappointed with them. Not that they cared what he thought.

Storm caused Mystique's change in appearance after the season one finale.
When Storm punched Mystique out in "The Cauldron, Part 1", the punch somehow "impregnated" Mystique's blue skin with Storm's African genes (considering Mystique is a shapeshifter, this could be possible), causing Mystique's true form to slowly undergo a subtle Race Lift, which was taken Up to Eleven after Mystique was knocked into Magneto's Enhancement Machine in "The Cauldron, Part 2". In addition to modifying Mystique's shapeshifting abilities, the enhancement also caused Storm's genes to spread through Mystique's entire body, permanently making Mystique's true form from season two onwards what is basically a "Black" version of herself. This could perhaps explain why, in the later seasons, her body and hairstyle look so different, her skin is a darker shade of bluish-green, her eyes are yellow with black pupils instead of white with gray pupils, and why Wolverine has such a hard time recognizing Mystique's scent: because Mystique's genes are mixed with Storm's.