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.