Instead of Khan in a sequel.. how bout...
Bring Kirk Prime into play, with Shatner playing him. But before you guys all snicker and say no.
What if Kirk Prime runs into Young Spock, and even Spock prime, and along the way both Spocks start to get a bad feeling about the elder Kirk and sense he is up to no good. From there you end up reintroducing EVIL KIRK from the mirror universe episode.
I don't care what anyone says, I always thought there was a huge opportunity lost when none of the other films did a movie with mirror universe characters and implications.
Shatner would be perfect playing the bad guy at this point in his career. Why try to replace the irreplaceable Ricardo Montalban/Khan character when you can do a story like this?