"The one idea that I loved, that I really wanted to do, was that Cyclops would build the Danger Room. Cyclops felt guilty, he felt that because the X-Men were too weak, they weren't strong enough, they weren't fast enough, that was the reason Jean died. If they were a little bit better at fighting, then she might still be alive. It was all about this guilt he had about her death and so he built the Danger Room to train them to be better. But in the end it really was about him not being able to let go of her, so that causes all the chaos and disruption in the movie. But in the end it's about him letting her go."
"Ultimately she kind of becomes that cosmic force that Phoenix is known to be, she choose to leave Earth and become 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 or her telling the X-Men 'I'll be watching.' Essentially she becomes a god."
Cyclops lives, Phoenix is an all-powerful god (who can make a return), the story makes more sense, Cyclops becomes the leader he should be, introduction, use and purpose of danger room explored - This is the movie we needed.
You should definitely check out the audio podcast (playable here) to listen as they talk about more X-Men stuff and a wide variety of things including Dougherty's thoughts on Superman Returns and the problems surrounding the release of Trick 'r Treat.
What do you think about Dougherty's plan for X3 - would it have made for a better film and happier fans?
With X-Men super producer Lauren Shuler Donner hinting that she desires and is planning an X-Men 4, as well as all of the statements from both her and Bryan Singer about him wanting to come back to the franchise, it's certainly a possibility to see Singer direct X-Men 4. Perhaps this is the chance for him to implement some of the unused ideas they had for X3. I think that would be a great way to right the ship and gain back the support of the hardcore comic fans and the film critics who laid a smackdown in the reviews of X3: The Last Stand and X-Men Origins: Wolverine.