I believe they should have a form of X-Factor in the movie. Or a type of mutant hunting government sponsered mutant group. Like Freedom Force of something the like. I think the Sentenials will be to hard to do. They would either look way to fake like the Hulk did or chezzy. Phoenix is a possiblity but should save it for the end. They need to have some time from her first not to rush things. Cyclops needs to quit like he did in the books after her death and come back.
I read an interview w/ Bryan Singer in Wizard magazine and he said that in the script he has been working on Gambit is a main character (but that it's possible that could change as the writing process continues)
He also said in X3 the X-men will be battling evolution itself (which we can assume means Dark Phoenix)
I'm guessing Jean will be the villain in X3 maybe coming back seemingly normal, but slowly becoming obsessed w/ her power and turning into Dark Phoenix
OR
Jean will just be plain good Phoenix and they will battle some other villain (ex: sentinels, apocolypse, juggernaut...)