Like a few have said, extend the cut with some of the deleted and alternate scenes - it would have fleshed out the movie a bit more.
Rogue was coming into her own in
X2, but that evolution into a sassier, stronger personality pretty much ended in
The Last Stand. I, of course, would have kept that and would not have her take the cure. Consider it? Yes. Take it? Never.
The Kitty and Bobby relationship subplot was entirely unnecessary.
I was not at all a fan of the Dark Phoenix effects. Demonic, corpse-like appearance? That's not the Phoenix.
I would have preferred if the Cure plot took a backseat to what the film should have been about the Phoenix. I can see why they put the Cure at the forefront - it made sense to the overall trilogy; First film - mutants trying to turn humans into mutants, second film - mutants and humans trying to end each other, third film - humans trying to turn mutants into humans. But I don't see why it was necessary to take devour most of the film when it easily could have made for a great subplot. The Dark Phoenix Saga is a far more important story to tell.
I quite enjoyed Cyclops' character in
X3... I just wished we could have seen more of it. And, even if his screen time had to be shafted (which it certainly shouldn't have, considering he played a
huge role in the Dark Phoenix Saga), they didn't need to kill him off. I understand that his death was supposed to drive Jean to insanity, but I'm pretty sure she was insane when she killed him. So, I really wished he could have had more screen time, but if he couldn't, I would have at least preferred he survived. This was, by far, my biggest problem with the film.