It seems like the speculation that the villain in STID is Khan has been going on since before the movie was even planned. I have one question for those of you who still support this theory: WHY SHOULD IT BE HIM?
What drove the drama in TWOK was the PERSONAL agenda Khan had against Kirk, an urge for vengeance that festered for 15 years on Ceti Alpha V after seeing his crew and loved ones destroyed.
At this point in the timeline, whether original or reboot, Khan HAS NO BEEF with Kirk. If Khan is the enemy, he'll be no more original than Nero: bland villain #230975 who wants to destroy the Federation... which according to Abrams seemed to be entirely localized on the Earth, including every starship in service (if they're not in the Laurentian system, that is).
If Khan is introduced in this capacity, it'll be lame. But personally, I don't think this is going to happen.
We don't know how old these characters are supposed to be. They could've skipped introducing Khan, played out that history off-screen, and have him a part of a plot, not the centerpiece of the story. If my instinct is right and this is going to be about Captain Kirk's mistakes, it could be a culmination of several missions that come back to bite him.