The thing is Singer and co. are in charge of the story. If something doesn't work it's because they wrote it that way. They seem to have gotten around Xavier exploding in X3 because they need Xavier for the story they want to tell. I can understand not having Jean or Cyclops back because they 'died'. Storm should be alive and well like Rogue, Iceman, and Kitty. If the character is left out it's because A) They didn't want her in or B) Another Nightcrawler situation where his role became so small that it wasn't worth having him in X3.