According to a source close to J.J. Abrams, the sequel to his reboot of Star Trek won't feature Khan but will focus on a character from the original 1960's series.
There is a certain synergy to Khan reappearing for the sequel to J.J. Abrams amazingly successful reboot of the Star Trek franchise. Many credit the second original film The Wrath of Khan as the best of its ilk and you could say that its success paved the way for the massive resurgence of Star Trek popularity in the 80s. Unfortunately, it doesn't look like we'll be seeing casting calls for a Ricardo Montelban lookalike any time soon. An anonymous source close to the production of the Star Trek confirmed that Khan will not appear as a villain in the film. Khaaaaan!
But there is good news. While the source did say that the film will not focus on a typical villain plot-structure, it will feature a character from the original series that ran from 1963-66.
"It's definitely a character that will make fans of TOS excited," he said. "Think along the lines of Harry Mudd or Trelane or Gary Mitchell or the Talosians or the Horta. Actually it's one of those that I named."
So there you go, the antagonists of Star Trek 2 will be one of the following:
Harry Mudd - A flamboyant space mountebank who appeared in two different episodes, the first of which has Mudd making women beautiful with an illegal substance called the "Venus Pill."
Gary Mitchell - In the second pilot of TOS, Mitchell was the helmsmen of the Enterprise and a friend of Kirk's who was struck by an energy field outside of the galaxy and received god-like powers.
Talosians - The bad guys in the first pilot, Captain Pike is imprisoned by these big-headed aliens who can implant illusions within the minds of humans. Definitely dudes you wouldn't want as your jailors.
Horta - A weird lifeform that is killing miners on Janos IV. In all honesty, this one seems like a longshot.
So, Trekkers which one is it? My bet is on Harry Mudd
Source: Bad Ass Digest