I expect it will be Khan. I would not be my personal choice but revitalizing existing material is what these writers seem to do best, so it might be the best choice for them, meaning in reality the best choice for us (the fans), since it is more likely to result in a good script and therefore a good movie.
They are going to make this film a "Dark Knight" of sorts, the movie that takes what was established in the reboot and introduces an iconic villain. Khan is the obvious choice, and probably the best choice from that point of view, as much as I would rather see something new in theory.
A couple of things to keep in mind, though:
1) I could see a re-imagined Khan being very cool. It doesn't really have to be the same character (think Jack Nicholson's Joker vs. Heath Ledger's Joker). It certainly doesn't need to be the same story. It might start like Space Seed, but as long as it goes in another direction from there, it could end up being pretty awesome. At any rate, the revenge element seems out of the question, so it won't be a remake of TWoK.
2) Khan might be the main antagonist, but there could be other new elements alongside of that. For example, after an initial scene involving the Botany Bay, the conflict could end up involving an alien world or civiliation we have never seen before.