One of the main problems for me about X-Men: The Last Stand was how Dark Phoenix basically contributed nothing to the climactic battle, but in retrospect, I think it kinda works. I mean, the idea behind Dark Phoenix in the movie was that she was evolving beyond really caring about the affairs of lesser mortals. Magneto wanted Phoenix as a weapon for his cause, but she didn't really care about his cause and that's why she didn't do anything.
I always thought that Jean really took to Magneto's line about pawns going first, and that she saw Magneto and the others as pawns to her.
What bothered me about Phoenix was that X2 already established what was happening to Jean. Magneto's mutant machine from X1 had affected Jean and was causing her powers to mutate. Cyclops says in X2 that she has been acting weird ever since Liberty Island.
Then X3 came along and ignored that. I really liked the idea that Phoenix was a result of a new mutation better than the idea that Phoenix had been in Jean's head all along and was being supressed by Xavier.
I think it can still work. Xavier suppressed the alternate personality successfully, never to be seen again. Then Magneto's machine cracked and undid the mental barriers that Xavier put in place. I think the problem, if it could be called that, is that no one ever linked it directly back in X3 to Magneto's machine.