I completely agree. Claremont deliberately chose the characters for the future part of Dofp in the comics because each served an important role in the story. I guess roles could be switched but I don't see why they should be when all of the mutants in the comic (Wolverine, Storm, Colossus, Magneto, Kate Pryde) all appear in the trilogy and would be alive during the future even in the movie-verse.
In fact the only character I feel they may need to switch would be the time traveller so it linked in with how they adapted the story aside from that. I don't see why they should change. I mean it would be a homage to the comics. especially if they add some of the iconic moments from that comic e.g. wolverine's demise.
I have no problem with halle Berry coming back. I don't think she's a bad actress at all and I'm positive with the right direction and script she'd play a good storm. Besides Storm is one of the most powerful mutants in the X-Men movieverse, if she died I would want to see that onscreen! it would be a cheat if we didn't get to see the fight she puts up before her death.