I re-watched "Space Seed" the other night and I was reminded that Khan was only seconds from dying due to a failing cryo-chamber.
A really cool twist on the original story and a bit of a middle finger to the fans who think they know what's going to happen would be to have Khan either die in this new universe or not be awakened at all. Another Augment (Joachim, perhaps?) could be awakened instead and turn out to be worse than Khan ever was.
That, I think, would make for a cool story. A brand new character who is really not a brand new character, made a central villain and perhaps a new Trek icon.