I don't like it (the Khan idea) because it seems a waste.
I don't think Team Abrams is going to want to give us more than three movies, regardless of whether JJ directs or merely stays on as producer. Maybe Orci and Kurtzman will want to stick around to work on a fourth movie with whoever comes in to produce/direct. I'd rather not go that route personally, because that just feels like the same 'diminishing returns' formula for the Superman movies of the 80s, or the Batman films of the nineties. But this is all speculation of course.
If I were JJ, I would pull out all the stops and set the current series to auto-destruct after the 3rd film, thereby forcing 'whoever' inherits the film franchise afterward to either reboot (again) or at least make another radical revision. Like what's happening now with Spider-Man. The prior ST films have had their ups and downs, but Paramount is playing a much bigger game this time. And it seems to me most film franchises aren't designed to sustain more than a trilogy, at most, before you either make a major change in format or start sliding downhill. Too often the third movie itself already shows signs of this decline.
But I've sort of gone off track here.
The Star Trek mythos in three movies. That's the project currently on the front burner. And Khan is a villian from just one episode, and one movie, out of almost 700 hrs of 35mm film. He's been done, the critics and fans loved him, and everone recognizes him. He's not a big enough component of ST overall to get his own film (yet again), and observers (fans and non-fans alike) would likely see it as further proof Hollywood has run out of ideas.
The villain/opponent shouldn't be any one particular individual we've seen before. They should instead really think of what are the central ideas/themes than embody ST, and work on building a new story from that. So that the movies together represent what is the best of ST rather than just particular elements copied over from this episode, that movie.
Of course if they DID do Khan anyway, I would still be one of the cautiosuly optimistic people. That's where I was when I first heard the creators of LOST had been given the keys to the car this time, and for me being optimostic has paid off so far... (and dammit! I can't believe LOST already started up again and I just missed it!)