Brett Ratner is tired of defending his directorial work in X-Men: The Last Stand, but fans continue to wonder what might have been if Bryan Singer had finished his X-Men trilogy, instead of defecting to Superman Returns. Michael Dougherty, the screenwriter for X2: X-Men United who joined Singer's defection, explained his ideas for X3 to Slashfilm in a recent podcast (transcribed by TheGeekFiles).
You found out was that Phoenix [(Famke Janssen)] was going round the world taking things into her own hands and that she had basically returned as a god, which they did in X3. She had viewed herself as above the conflict, that she was here to end things on her terms, she was sick of the fighting and
she was going to take things into her own hands and she did not give a s**t what the X-Men or the Brotherhood had to say about it.
And ultimately the way it was going to end, at least the version I was pushing for ... she kind of becomes that cosmic force that Phoenix is known to be, she leaves Earth and becomes a god, or at least a higher level of intelligence, and she goes into the cosmos possibly to kick-start life somewhere else. The final scene for me would have been her telling Cyclops [(James Marsden)] or her telling the X-Men "I'll be watching."
Dougherty also planned a different outcome for Rogue (Anna Paquin).
The whole point of Rogue's character is that she is supposed to come to terms with who she is and also I don't think it's good to tell girls "Yeah you should change yourselves so you can get a guy."
Instead The Last Stand saw Rogue lose her powers, Cyclops die, and Wolverine (Hugh Jackman) kill Phoenix, all to the disappointment of the fans.
You can check out the entire podcast here.