actually it's pretty simple... X3 showed magnetos powers slowly returning at the end.... So the cure was not permanent like they thought. So Magneto, Rogue, Mystique, all get their powers back in time. That sets up Mystique finally being independent of Erik, and Rogue possibly screwing up... (imagine her touching someone with powers, when it kicks back on... the person screams, rogue screams... she can't let go), the person dies, or goes into a coma... and rogue has those thoughts, and maybe a new power set stuck in her).
Xavier is placed in his twins body as shown at the end... so he returns
While Jean probably shouldn't be in the film... I'd have Havok (father or brother depending on FC) come to the X-mansion in search for Scott... they inform him of his passing but he refuses to believe it due to a message he received. We later find out that Phoenix didn't kill scott... but placed him in her telekinetic cocoon at alkalai lake, taking her place there. We find out much later that the villain of the film (Sinister) now has scott, and is using DNA from the mummified remains of the worlds first mutant (En Sabah Nur) to create 4 super mutants. The project is called "apocalypse" and the 4 are the horsemen.
there's X4