1. What exactly was Phoenix's motivation? She was the id ok, so she does not need to have much motivation beyond random destruction. But why did she stand on the sidelines throughout the entire final battle? Why did she even bother going along with Magneto's war to eradicate the cure in the first place? It all seemed to be beneath her.
Her motivation revolves around control. Because, as a personality, Phoenix had been stifled and held back (Xavier's mindblocks) now the thing she fears is others trying to control her. It's in every scene, from the early ones with Wolverine, to Xavier, to Magneto. Jean even kills Cyclops due to a loss of control and an inability to control herself. She kills Xavier because she thinks he is trying to control her.
Dark Phoenix makes it clear to Magneto that she will not be controlled by him in the camp, and he catches onto this and almost immediately shifts her attention to the common enemy of humanity how? By explaining that humanity means to control mutants.
The reason she doesn't act until the very end is, aside from budgetary reasons, that she doesn't NEED to. She just wants to be left alone and to be free. She has not, in essence, really yet chosen a side in the conflict.
It is not until Magneto appeals to her after being "cured" that she begins to act. Because she sees humanity wants to control and diminish mutants, and because they are now actively trying to do so to her (the dozens of cure darts the military fires at her).
In the end, Phoenix is a selfish force, and she doesn't act until she is personally affronted.
2. How on earth did Pyro switch from nuanced rebel to cartoony 'I WOULD KILL XAVIER IF YOU ASKED ME TO' villain?
Where was he ever portrayed as a nuanced rebel? He walks away with Magneto in X2. That's "nuanced rebel". Pyro was clearly indoctrinated, and young and headstrong when he makes that comment about Xavier. Magneto recognizes that Pyro doesn't fully understand the war he's part of, and sets him straight.
3. Why did Xavier not grieve, or show any emotion at all really, for his prodigal son Cyclops?
Because the writers chose not to include this. They probably should have. Aside from that, there were much, much bigger issues to deal with.
4. Why did Mystique betray Magneto by giving away his location to the government? For petty revenge? Or was it something she cooked up with Magneto considering it was a ruse anyway?
Seriously? Because she was loyal to him for years and then he abandoned her. The film flat out says "Hell hath no fury like a woman scorned".
5. Why is Magneto so shocked when Jean finally unleashes her wrath on Alcatraz, knowing full well what she can do and actually banking on it for the final battle?
Because, he didn't truly understand the nature of her power, and didn't realize that she could become THAT powerful. He certainly didn't expect his actions and his attempts to manipulate Jean to put both humans and mutants in peril.
6. Rogue taking the cure may fit her prior characterization, but it is an absolutely terrible message to send to viewers. If she chose to take the cure on her own terms fair enough, but it was pretty clear she was motivated largely by the love triangle between her, Bobby and Kitty (which wasn't even a triangle considering Bobby and Kitty were just friends at that point). The message is basically 'Change yourself for your man'.[/quote]
"Make your own decisions" is a bad message to send to viewers?
You may need to watch that scene again. She flat out says she did it for herself. The film addresses this obvious concern by having Logan caution her not to do it for "some boy", having Bobby say he didn't want her to do it for him, and her ultimately explaining that she did it for herself.
