Recycled Script: Eagle-eyed fans have noted that Sublime is quite similar to an old Avengers villain called "That Which Endures," another ancient, microscopic sentient lifeform that claimed to exist in all living things and to have guided evolution and attempted to control mutants. However, they have rather different modi operandi (That Which Endures wanted to make the jump from humans to mutants, whereas Sublime wanted to destroy mutants because it could not make that jump) and separate entires in the Official Handbook of the Marvel Universe, throwing the idea that Morrison intended them to be the same character (if he was even aware of That Which Endures at all; the story was very obscure and didn't have anything to do with the X-Men) into doubt. A somewhat similar character also appeared in the final issue of X-Man.
Screwed By TheEditors: When Morrison first got the book, he stated that he wanted to have a run at least as long as Claremont's first: seventeen straight years. He lasted three, due to getting into a fight with the editors over the creative direction of his character Marvel Boy. The differences proved irreconcilable, and before long Morrison did the unthinkable: he signed an exclusive with DC. Naturally, he hasn't been seen at Marvel since, and what's more, many of the changes to the X-mythos he made were quickly retconned or swept under the rug, a move Morrison himself reportedly believes was done to spite him for leaving.
Grant Morrison originally wanted to include Rogue in the team's lineup, and planned to base her appearance and personality on her portrayal in X-Men: Evolution.
He also intended to have Colossus on the team, and for Moira MacTaggert to take Beast's scientist role. Their deaths in the Legacy Virus storyline prevented this, resulting in Beast being transferred over from Claremont's X-Treme X-Men. Likewise, he gave Emma Frost her secondary diamond mutation.