Perfect ending for X-men 3
For us X-men fans, we'll never know what Bryan Singer and his writing team (Michael Dougherty, David Hayter, or Dan Harriswould) would have made for X3.
However, I do believe they would have written a better conclusion to the "Dark Phoenix Saga" that was both respectful of the original comic book and make it even better. Here's a quote from one of the X2 screenwriters on the DVD commentary:
“In the [comic] book, it’s such a beautiful moment where it’s just her and Cyclops. And she says ‘I got too much power; I can’t handle it; I have to go.’ She basically uses a giant gun to kill herself right in front of Cyclops. I wanted to take that one step further and have her bring Cyclops up to her. And say, “I can’t be allowed to live; I can’t allow this to go on.” She uses Cyclops’s own beams to destroy her – which I think is what made the studio nervous about doing it because it was really disturbing, upsetting, and psychologically scarring for Cyclops; but I knew it would kick ass for the X-Fans. So like I said it got cut along the way.”
I'm pretty sure they mean that Jean would remove Cyclop's visor and telekinetically force Cyclops to open his eyes. So Cyclops is helpless and has to watch himself kill the woman he loves.
The X2 screenwriters cut this scene from X2 because they felt that "Dark Phoenix Saga" was too soon in the movieverse and because of Fox's hesitation. I do think this would be a greater, better and sadder ending for Jean destroying herself rather than have Jean allowing Wolverine to kill her.