There’s been a hell of a lot of speculation recently regarding just what villain Benedict Cumberbatch is going to play in the upcoming 2013 Star Trek film. And while the initial rumors were that he would play a young Khan, recent comments have caused the Trek fandom to consider other alternatives for the villain. Based on some of the stills that have been released from the set, and some of the things that the production crew have said, we know a few things, most notably that he is not playing an alien (or if it is an alien, it’s one that is human in external appearance).
Another Genetically Altered Human: Khan isn’t the only genetically engineered human out there, and it’s quite likely that there were augmented humans in Starfleet in this alternate timeline. It would be interesting to see a different story based on a similar vein.
Evidence to support this claim: Cumberbatch was rumored to have put on a good bit of muscle for this role, and genetically altered humans are said to be stronger than humans. This is something that we see evidence of in the leaked stills, as he holds his own against Spock:

Location Shot - TrekMovie.com
The psychological issues that result from the augmentation process make for interesting, brooding sort of villain, and numerous members of the Star Trek production have stated that Heath Ledger as The Joker in “The Dark Knight” was what inspired their latest villain. It would be interesting to see how others fared under the same sort of conditions. There’s also room for the argument that Cumberbatch IS
Hesitations: I’ll repeat something that was said in the original article that cast doubt on Khan – “There are a lot of directions we can go in the film and in this particular case we chose to do something that would be original and unique and different and again on paper I think we made the right choice.” Unique… different… after Khan, I don’t think that a genetically engineered human could be that unique. It would be a huge cop-out and would likely disappoint fans. Also, there’s been no evidence thus far to suggest that a genetically altered human can resist a Vulcan neck pinch, something I’ll get to in a moment.
Gary Mitchell: Gary Mitchell was from a family with known esper capabilities. He himself displayed rather impressive numbers on various tests of esper abilities, and could even participate in telepathic discussions with some telepathic species.
Evidence to support this claim: The scenes that have been leaked of Benedict Cumberbatch as the villain show him in an outfit that is very similar to the outfit worn by the other crew pictured. It has been speculated that this is either a uniform variant, or perhaps the Academy instructor uniform without the top “tunic” part.
The original casting choice for this villain was Benecio Del Toro, which is quite interesting given the fact that he is quite a bit older than Benedict Cumberbatch. Still, both bear a passing resemblance to Gary Mitchell:

Gary Mitchell was friends with Kirk in the Academy, so running this plot-line or a variant thereof would allow us to see a bit of emotional depth out of Kirk. In the TOS episode that featured Mitchell, he developed extraordinary powers, which could have included the ability to “shrug off” a Vulcan neck pinch:

Neck Pinch - TrekMovie.com
The photographer that captured this image indicated that Cumberbatch continued fighting after this, which is why fans speculate that whoever the villain is can resist a neck pinch. It’s possible that the galactic barrier might also have increased his physical strength, or that he could psionically enhance his own strength.
Hesitations: Gary Mitchell was a one-shot character. It would come as a surprise to me if they chose a character who was only involved in one episode of the Original Series as a 2013 Movie villain.
Q: My initial vote was actually for Trelane once fans began considering someone other than Khan. But I think Trelane wouldn’t be caught dead in the outfit Cumberbatch was wearing, so for now I’ll list my thought as a “weak Q.” At first I was thinking perhaps a young Q, but neither a young Q (nor Trelane, for that matter) would have the sort of brooding insanity that was embodied by Heath Ledger’s Joker. It would have to be a Q that wasn’t fully in control of himself though, else Spock wouldn’t be able to get him down on his knees at all.
Evidence to support this claim: Q can resist Vulcan neck pinches, and are stronger than human average. Q are a species that fans have often wanted to learn more about, and while John de Lancie’s Q seemed to harbor affection for the human race, a brooding, conflicted Q would be a fascinating thing to see. Also, they have a penchant for running around in Starfleet uniforms.
Hesitations: As awesome as I think that a Q as a villain would be, the production staff has indicated that this will be a very action packed film, just like the first. Q plotlines typically involve more talking than things that go boom.
Augment Klingon: Ever since Enterprise explained the decades old debate about what was really up with TOS Klingons, the explanation has been a subject of controversy with many fans. Still, perhaps this will help to breach the gap a bit.
Evidence to support this claim: As I’ve mentioned, Cumberbatch was seen in a Starfleet variant uniform. It would be interesting if part of the “augment lore” involved Klingons disguising themselves as humans to infiltrate Starfleet. It’s a new twist on an old classic (Romulans, Changelings and others have infiltrated Starfleet prior, after all). Also, he’s stronger than the average human. Yes, this isn’t really “evidence” just something that would be quite interesting. Rumor has is that Klingons will be featured in the new film, although I was at a loss to find a good source for this information. Part of the shoot took place in Hawaii, and we know that there is a scene that involves a volcano because of this still:

Spock in Volcano Suit - TrekMovie.com
There has been discussion on various forums that the scenes shot in Hawaii were meant to represent Qo’noS, and there are some rather inhospitable volcanoes there.
Hesitations: There’s been no evidence to support a genetically augmented Klingon being able to resist a Vulcan neck pinch. Most of the evidence is based on hearsay and speculation.
Other thoughts that I had involved something like Section 31, as the whole espionage angle would be interesting, and it would certainly explain why he’s in a Starfleet uniform. Section 31 seems to be hotly debated by fans, though, as some feel that it’s not in line with the mission of Starfleet. Someone from the Mirror World was another concept that I saw referenced by a few fans online (especially because of the 2 other variant uniforms that have leaked online) but it makes little sense to me. If it was really the Mirror World, evil Kirk or someone would be the antagonist. In the past, the intrigue of the Mirror World was that you saw “good guys” do bad things. Beyond that… this universe is already an alternate universe.
It’s going to be interesting in a few months when we first start getting the hints of the new teaser trailers. Perhaps Cumberbatch is playing Khan, and they’re going to make him drastically different than the Khan we’ve all known and loved. Either way, I’ve got my fingers crossed, and am chanting a mantra of “Please don’t suck.”