I'm still a fan of the idea that the Jean in The Last Stand
was actually a clone of the real Jean created by Mr. Sinister (basically Madelyne Pryor), and while "Jean" thought she vaporized Scott, she actually teleported him to Mr. Sinister's location, where he's been performing experiments on both him and the real Jean Grey.
But that would probably require a plot of which Wolverine (or Xavier and Magneto, if you include First Class
) isn't the main focus. Crazy, I know.