The plot synopsis released from Paramount says that the crew of the Enterprise deals with a threat from within Starfleet. So, that rules out Khan, as he was never in Starfleet. However, I prefer not to speculate. It could be Mitchell, (it could be Garth of Izar
) or maybe they'll even surprise everyone and go with a new bad guy. After all, the villain in the last film was a completely new character.
Besides, in that comic, Mitchell dies, like he did in WNMHGB. I have no idea if they're going to even consider what was done in the comic, or ignore it entirely, as has typically been done in Star Trek.