I view Admiral Marcus as the main villain of this movie. Sure, Khan was there, and he definitely became a menace, but he wasn't really
the bad guy. Khan was just another big superweapon gone awry.
I will say, though, that I would have loved a scene in the beginning of the movie of a starship discovering the Botany Bay. I think that would have been more fun than the unnecessary John Harrison "twist" in the brig. "I'm not really John Harrison. I'm actually Khan!" Who cares? Just have him be Khan from the get go.