I've been saying since we first saw Cumberbatch fighting Spock that I think he is playing a Klingon infiltrator. I can't imagine a movie called Into Darkness about a more personal-level villain like Khan or Gary Mitchell when the producers have said that the events of this film will thrust "everything" into a darker light a la Empire Strikes Back. Klingons are a galaxy-level threat.
Consider too that Benicio del Toro was originally supposed to have the role. Dude looks like a TOS era Klingon to begin with.