I don't object strongly with the Phoenix explanation in TLS. It's not what I would have expected after X2, and it calls into question exactly who Jean has been in previous films after Xavier tampered with her mind; but it's an efficient way to tell a Phoenix story in the film universe. I do dislike how she is used within the film though (or not used as it were)
It certainly wasn't what I expected either. But then again, at the time, I think it was expected that Singer was going to come back, and do
X-Men 3 and
X-Men 4 together, and we probably would have gotten more of a Phoenix Saga transitioning into the Dark Phoenix Saga. Then Singer walked, and Fox decided they wanted to kill the franchise (business wise, I don't exactly blame them, as the movies were getting more and more expensive. They made a business decision to end the huge investments)
As far as how Jean was handled in the movie... I like the characterization. I like what they did with the character, and I thought they portrayed her well as Jean Grey going crazy, for lack of a better term, and being consumed by these powers that she wasn't used to, and spiraling out of control.
I didn't have a problem with her being a "mute" for the latter part of the movie. I was able to fill in the blanks for her motivation to go with Magneto, as well as her lack of action at Alcatraz. I know a lot of people had issue with it, but I was able to put it all together, and it worked for me.
There are also 2 deleted scenes from the Alcatraz battle that clear up a lot of why Jean did what she did at Alcatraz, and why they were cut, I'll never understand because they combine for about a minute and a half of footage, but do so much to help explain her motivation.
I dunno. When I was reading the Dark Phoenix Saga the other night, and when I was watching the animated series' version of the Dark Phoenix Saga a few nights before that, so many times I saw parts where I was just felt like the movie version connected so well with it. I was surprised, because so many people say that the movie totally ruined the Dark Phoenix Saga, and previously, I had only really skimmed over the story, or it had been so long ago since I had watched the cartoon, that I wasn't fully familiar with it. But reading it again, it certainly is a different direction on the story, but I feel like they pushed a lot of the right buttons.
Even one of the most jarring changes, killing off Cyclops, when in the comic he's the one that has the psychic rappart with her, and he's the one person she is unable to kill, even that alteration has a way of working itself out when in the comic version, it's her watching him struck down in the final battle that finally sets off her powers once and for all, before she kills herself, and in the movie, it's her striking him down, and her killing him, that sets her off and eventually leads to her wanting to be killed. Even though Cyclops got shafted in the movie, I still felt like it was the Jean & Scott connection that drove her motivation, and with that, I can accept that.
The changes on the surface are very jarring, and devisive amongst fans certainly, but at least for me, when you dig beneath the surface, I think the film's version of the story hits all the same notes.
I wouldn't argue that they couldn't have developed it better though. They certainly could have, and that's where even though the movie as a whole works for me, and may even be my favorite of the entire series, it does remain an underwhelming movie when you consider the potential of what the movie could have been. And that's not saying "what would Singer's film have done", or "what would Vaughn's film have done" - the movie, as is, had potential to be better than it was, and didn't need Sentinels, or a lot of other missing elements to do it. It just needed to expand on the elements it did have.
I think this movie is a case of some slight alterations would make drastic changes.