Well, for starters, the script would have been written in a way that would have made it impossible for this film to be less that 2.5 hours...............
Ok, Cyclops. If I had my way, he would have been one of the principle characters this time around, but I do understand the fact that he was busy making Superman (cough............bastard............cough). So, with that in mind, we would have not seen the creepy skin crawling effect at Alkali Lake. They would have been kissing, Jean would have opened her eyes in some evil manner, and immediately we would have gone to Xavier's pained expression (amidst the sound of Phoenix scream of course). Cyclops would then be AWOL. Jean of course has no memory of what happened to him, and neither for that matter does Phoenix. Phoenix believes she has killed him, but is slightly confused over the matter due to Jean's influence. Cyclops would then have reappeared at the end battle. If Jean had to die, it should have been Scott that killed her. If Logan has to have some major part in this, he could have done exactly what he did in the 90s animated series. Cry about it. That's emotional!
As for Angel, I would have ensured that there was a reason for him going to the X-Men for help. Also, I would have used the beginning Danger Room sequence to my advantage. What the hell was wrong with the idea of Warren taking up some emergency training in the DR? He overhears that there is going to be an attack on his father, he wants to protect him, the X-Men are short on members, so why the hell not?
Rogue. Do not even get me started. WTF did they do to her and why? The little screentime that she had pretty much portrayed her as nothing more than a moody *****. There wasn't really any screentime devoted to showing her turmoil over the cure. I would have written in a far more emotional reaction to her discovery of the cure's existence, and I would have definately written in some form of backlash to Storm's pretty callous (and may I say out of character?) comment about there being "nothing wrong with you."
And, I know it's been said before, but in my script, Rogue would have been present in the final battle.