X3 has some interesting ideas and great moments, I would argue the image of Wolverine painfully passing through the death storm to kill his love is very powerful, but overall the picture fails because it tries to do too much with too many characters. Perhaps a more competent director could have kept all the plates spinning and made a good show of it, but whatever the reason Ratner doesn't succeed.

And to add to his problems, one of his key plots (Phoenix) is wholly uninteresting because the character change has already happened off screen. Jean Grey is already 'full Phoenix' when she first appears and her character crosses the line within seconds as she murders the man she loves most. There's not really anywhere else to go after that and the subsequent handling of this murder is superficial at best, there's no great internal struggle with the power. The rest of her story is just about other people being afraid of her and using her, or her just looking/being evil for no real discernable reason.

Then you have the fact that this main story has very little to connect it with the mutant cure plot. Sure, Jean Grey is physically present in the attack on the island where the cure is located but thematically, her power isn't tied to the cure.