I vote Harry Mudd, if only because then I would understand all the secrecy.
J.J., "The villain is Harry Mudd!"
I could easily see:
Mitchell, Khan, Garth--for obvious reasons already stated.
Kodos--for similar reasons though he seems to not be all that popular a guess and I was under the impression he was a bit older than Kirk.
Trelane--because it would be such a radical difference to the character.
And just because I can....
Jean Luc Picard--who is very, very angry that he was erased from history so he's teaming up with Gary Seven who has time travelled forward from his home in the 20th Century to fix the timeline.