Wonder why Jean Grey suddenly went psychotic with the power of the Phoenix in X-Men: The Last Stand? She has been trapped under water for an indefinite period of time, and in addition to her schizophrenic personality being released, it's quite likely she suffered brain damage.
Some fans chalked up the lack of Cerebro to just being something cut for time. However, you'll recall that in X2, Stryker stole either the entire thing or most of it, and that Nightcrawler couldn't take any of it with him when he was getting Storm and Xavier out of the Dark Cerebro room.
One of the commentaries in X2 (possibly inadvertently) lampshades this, joking that after the horrible experiences Xavier had in the first two movies, Cerebro would be turned into the swimming pool. Think about it, first the sabotage by Mystique in X1, then being trapped in his own head and subsequently mind controlled into nearly killing first all mutants, then the rest of the population. He's got to be sick of it by X3!
Magneto's plan seemed...well, not very well thought out. I understood his tactics, but his using "the pawns" as human (mutant?) shields and wasting literally hundreds of mutants went against Magneto's belief in mutants being precious and better than humanity. Then I remembered Erik has just lost the two constants in his life, the only true companions he had since the camps - Mystique to the Cure and Charles, his oldest friend, to the Phoenix. Of course he's going to have a weak plan, he's thrown it together while he was angry and upset.
Hank's disgust at something he himself once tried in the third film makes perfect sense: when he joined the others in the hanger, and they still accepted him, he realized Raven had been right the night before.
Magneto abandoning Mystique after she's depowered is still callous, but also makes a certain amount of sense; Magneto is pushing the "mutants must defeat humanity" part of his mutant supremacy doctrine harder than ever. If he's seen associating with a human, even a depowered mutant, it could seriously undermine his credibility and ruin his influence — which, in turn, would cripple the army he's trying to build to protect all of mutantkind. He's still an asshole, but he's making his decision on the basis of The Needs of the Many — and Magneto has always prided himself on being the practical, realistic one when compared to Xavier.
The Professor and Magneto go to Jean's childhood home where she is waiting for them. No one else is seen in the house beside these three, and considering that Jean's parents must have still lived there, due to their surname 'Grey' being on the mailbox afer 20 years or so... this means that after arriving at her old home, Jean (or rather the Phoneix) killed and vaporized her parents...
We don't know that they were home at the time.
On the subject of the cure, it is very likely people will still be ostracized because they were mutants at some point. Imagine someone being seen to get it and get attacked later, now without having their powers to protect themselves.
The cure as a whole becomes horrifying when you consider the whole "mutants as metaphor" aspect of the films and comics—it can be compared to the concept of "curing" different minority groups, most obviously LGBT and disabled people. This can make it really horrifying for people in those groups when the cure is actively forced on some, and many others are pressured into taking it when they don't want to...