I'm trying to keep separate the concepts of "could have" with "would have". Professor X COULD mentally rape anyone on the planet yet wasn't perceived as a threat. Just because someone has great power doesn't mean they HAVE to use it for evil and destructive purposes. Jean COULD have levelled entire cities when she retreated to her family house and killed everyone in her path, but didn't. The fact that her attacks were so well focused - even when she went berzerk at Alcatraz she seemed only to kill the bad guys - does show a level of control and hints at something just a little deeper. Even the book shows she was more in control of herself and aware than what you're willing to give her credit for. The only major piece missing that would have brought her back or wanted her to come back was the fact that she was convinced that Scott was dead and that it was her fault and with such blood on her hands she wouldn't be able to live with herself. If that's the case, then I say we put that missing piece back into the puzzle and solve this problem.
Yes, and there being no good side to her, no Phoenix, that is the problem. The mental blocks were a last-minute hack introduced when they ralized the movie was downscaled so much that there was no logical or creative way to account for her going evil. So might as well make her evil from the beginning and start killing everyone off. That oughta shock the audience good. No argument with her being a monster. My claim is that's not how it should have been portrayed in the first place. I don't want to defend or justify it, I want to expose it for the flaw that it is.
Furthermore, connecting her mental blocks breaking down to Magneto's machine is false and unnecessarily complicated. As I said before, if her mental blocks were collapsing, then not only would her power become stronger but at the same time you would have to start seeing more and more aspects of the Phoenix persona come forth since that was being held back as well. But we didn't. You didn't see any personality changes. She was still the same lovable Jean until the end. No frenzied rages, no sudden bouts of anger, no evil-eyes and forks and knives being hurtled at people, no resentment towards Xavier or anyone else that she was shown to hate later in X3.
But back to Magneto's machine. First let's be clear on what it is exactly that Magneto's machine does: it triggers mutations in people who haven't had them yet. It activates inert X-genes or modifies the DNA to make those genes active. That's that, in a nutshell. It was assumed that the machine would not affect mutants as there was nothing that needed to be triggered, but they had no way of knowing. In fact, that's exactly why it would affect Jean, because she was an exception. As she personally stated in X1, mutations are triggered either by puberty or extreme emotional trauma. In her case it was emotional trauma, when her friend Annie died. Her mutation appeared before its natural time, and for whatever reason her evolution was incomplete. Magneto's machine would have therefore triggered it again and let it run its course. Again, this machine affects genes, which are directly responsible for the way that a mutant's powers manifest themselves. Mental blocks are artificial locks placed in a person's mind. They are not related to anything that the machine was designed to do and did. No other mutant present was affected, because everyone there had mutations that already ran their full course and reached completion. All except Jean's mutation, which was triggered early and never finished.
It would make much more sense and be much simpler to simply state that it was Jean's death, her willingness to give up on life, that final moment as she panicked and cried out which dropped the mental blocks if there were any, allowing her Phoenix persona to take control, and with its bitterness and will to survive, allow Jean to overcome her ordeal. Several mental trauma can do that to a mind. It affects different people in different way. Sometimes it makes an evil person have a change of heart. Sometimes it releases repressed or multiple personalities. Sometimes it makes a person humble. Other times it destroys the entire mind and you end up with a block of wood. Using that to release the Phoenix persona I can see that. And it would actually be somewhat related to the comics, except that this second persona did not come from an intergalactic energy entity. But the comics make things unnecessarily complicated. Singer's idea was to keep things simple, manageable, and consistent. Therefore it is my believe that the above Mutation Machine trigger is the simplest and most consistent way to explain what happened to Jean, and it violates nothing established in the first two films, unlike the mental blocks / angry persona idea put together by Penn and Kinberg, which throws all that happened in the first two films, which I already discussed and explained in detail, out the window.