I gotta be real: discovering who the villain is after all, I do admit I was disappointed. With a whole new version of the Star Trek universe to play with, I was hoping for something more satisfying than Khan. I'd almost have rathered 'John Harrison', a brand new villain. Regardless of what is done with him I can't help feeling that falling back on Khan (or any specific former villain for that matter) was a creatively bankrupt move on Orci and Kutzman's part.
Oh, but that's the nice thing about this universe's Khan: he isn't the villain - not really. He's still a genetically engineered superhuman with a special
moral compass. But he's out to save his people - using really violent methods.
Admiral Marcus is the real villain in this film. If he'd succeeded with his plan to spark a war with the Klingons, the resulting death toll would have dwarfed the one caused by Khan.