Of course we also have information that Peter Weller is playing Admiral Marcus, Carol Marcus' father. If that's true then my next guess would be that, in this timeline, the Botany Bay was discovered by Admiral Marcus years earlier, but instead of turning Khan and his followers loose on Ceti Alpha V, Marcus did something else with them. Maybe he imprisoned them or locked them away in a secret laboratory somewhere, or maybe he wound up killing everyone but Khan. Somehow Khan escaped, took on the identity of John Harrison and quietly plotted his revenge.
HELLO! Wow this is the best most logical theory for Khan when you consider all the facts we have so far. I really like it.
Makes sense. Admiral Marcus (who's said to have a ship / be CEO) finds Botany Bay...maybe because of Nero / paranonia, Starfleet (maybe Section 31) says "hey if they have technology from the future to blow up planets, we need to re-think about everything we've done, including putting those genetically engineered freaks on that sleeper ship".
So Admiral Marcus goes and gets the ship, and let's say it's Khan and all of them and somehow everyone is killed but Khan. Perhaps all of Khan's followers blow up the ship as a diversion to get Khan out....so Khan could be floating around Space, gets picked up by the Klingons. Khan then escapes that as well and is like: "200 years ago I was prince, etc and now the people from Earth tried to kill me and/or killed all of my family, so now I will return to Earth to 1) get my vengance on Admiral (Admiral? Admiral. Admiral!) Marcus...which he does by trying to kill his daughter Carol, who by this point would have gotten the eye of Kirk and then rest of the movie takes place. And 2)wants to show everyone who sent him away before that they need people like him, so he starts sabatoging/blowing up everything, similar to the bad guy from Live Free or Die Hard, where he was a specialist in security and found all these holes but no one would listen to him so he has to go out and show everyone how dangerous it really is, and that someone like him, Khan, should be the ruler/prince of the world, etc.
But he can't just walk around and say he is Khan, so he spends most of the movie as John Harrison, a starfleet cadet, etc who minds to himself. Then when the time is right, he shows who he is. Perhaps after a few detonations of the fleet, people are like WTF is going on. Then Admiral Marcus admits to Kirk/Carol that he did a bad thing many years ago and this could be the result of one man getting his vengance...and then that's when John Harrison reveals himself as Khan (maybe its near / at end of movie)
Wow that would be awesome. A fresh new take on the iconic villian of the franchise....kind of like Joker in Nolans Batman