The day I saw the movie, I posted this in a forum as a suggested alternative to show it could be done. MASSIVE, TOE-THREATENING SPOILERS!
Let the movie open as it did.
When Wolverine stops Scott and pushes on how they have to get past Jean’s death, let Scott blast him a few times. Let us see that a) Scott is not handling things very well, and b) he’s a powerful mutant who can take out Wolverine (as he has in the past). Afterwards, when someone makes him stop, he can say the “not everyone heals” line.
They hear of the cure, Storm does her “it’s not a disease” bit, but Rogue blows up at her instead of being more or less dazed the whole movie. “At least you can touch someone, feel them touch you! Of course you like it, you’re better than human. Some of us are less.”
Scott hears Jean, goes to see the lake, she arises. Not as Dark Phoenix, but as SuperJean, more powerful than before.
He brings her back to the mansion, where she explains how she must have protected herself. Just before the flood hit she felt so powerful, she doesn’t know why. Xavier explains to her about the shunts he placed in her mind. She’s not sure how to feel about that, and neither is Scott.
Angel escapes from his father, flies to the mansion.
Magneto collects powerful mutants, let that subplot go as it was.
With Angel’s information on what’s goiung on, the X-Men are proactive, helping to subdue riots at the clinic and trying to track down Magneto’s army. Jean is immensely powerful, and it’s getting to her a bit. We see some of the wild side. Scott is deliriously happy; he has her back, we get lots of romance. Logan is a bit disgruntled and continues to flirt with her, and is surprised when she flirts back. We’re starting to see a darker side of her.
The Mystique rescue, as seen. Except Jean and Logan arrive to prevent it. In the battle Jean loses control and we see the Phoenix effect for the first time. Magneto and minions get away, barely. Jean jumps Logan, who goes along with it until she calls herself Phoenix and he pulls away. She is confused and asks for Scott when the surviving guard shoots her with the cure. She stops it mentally and goes totally Dark Phoenix on the guard, killing him. “How dare you!” and so forth. She flies off.
Wolverine gets back to the mansion and fills them in.
The X-Men fly off to stop Magneto’s army. Much like before except Xavier and Scott are there. Scott is yelling tactics, trying not to think about where Jean is, and Xavier is fighting Magneto using mind control of Magneto’s own minions. After a grueling battle they win, except Jean shows up in full Dark Phoenix garb and takes them all out with ease. Including Xavier, whom she blasts big time (kills, if we really must). She’s ready to blow the place up but Wolverine and Scott work together; Wolverine distracts her while Scott gets closer, and Scott and Jean have a moment where we can see Jean fighting to regain control. She tells Scott what he has to do while she can keep her defenses down and, screaming, he blasts her.
Epilogue – Scott has to leave for awhile. Storm takes over as leader. Keeping the school open is made easier because Angel is rich and offers to underwrite it. And life goes on.
All in all, dump some extraneous scenes and add in the fifteen minutes to make it a 2 hour movie, and this could have happened. Or something better, I’m not a screenwriter. But at the end I would have cried for Scott, I would have cared for Jean as a person, I would have felt Rogue’s anguish, I would have felt Wolverine’s pain at being an outsider to a relationship once again. The characters would have had some depth.
My two cents.