They can redeem X3 and can easily bring back Scott and Jean. Maybe even have the Blue and Gold teams.
We already know the cure is not permanent as Magneto's powers were returning so Rogue could return. It would be great if they brought in Gambit (Taylor Kitcsch) since they are already disregarding elements of Wolverine from Cannon.
Sinister could have found Scott and held him in a location shielded from Cerebro (possible, since Magneto's helmet also masks from Cerebro)
The resurrected pheonix could be a different Jean. Much like the comics, the real jean could still be in a cocoon in the lake. And with the ability to manipulate molecules, she could have easily manipulated a clone of her body.
Maybe Sinister has them both? That he, too, was drawn to Alkali by the rise of the PHoenix. Found Scott mid-kiss. Attacked Phoenix and took Scott and the real Jean.
I would love to see James Marsden play a significant Cyclops role in the next film. Now that Logan has his own franchise, he doesn't need such a large role in the ensemble.
I don't think they will ignore X-Men Origins: Wolverine.
I think it would be great to see Sentinels, but with X3 ending with a mutant ambassador to the UN, I don't see how a drastic turn towards sentinels would work... unless a massive mutant uprising escalates fears but that would just repeat X3.
I open this thread (mods closed if i'm wrong) because of this:
http://www.obsessedwithfilm.com/movie-news/producer-says-x-men-4-5-in-active-development.php
Producer Lauren Shuler Donner revealed:
So it looks like X-Men 4 will happen.
"I know so little about First Class. Im still happy theyre making the X-Men movies, and Fox is smart they can keep making these movies with the wealth of back story you could do a spin-off of every character. The challenge of the first was having ten to fifteen characters and having enough time to establish who they are, especially with the years of back story. But I dont look back and feel any disappointment. Id love to come back and do a new one with the original group, but theyre busy."