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.