The Website
badassdigest.com source wouldn't specifically say which villain will be featured in the film, but they do name five possible choices. And they say one of those five villains that were in the first season of the
Star Trek television show will be the main baddie.
Just to keep track of all the rumors so far we have
Latino Review claiming the main bad guy is Khan, then hours later JJ Abrams said Khan will not be in the movie. We also have cast member Simon Pegg saying that he has seen the script and claims that Khan wasn't not in it. While the most popular Brazilian fan site for
Star trek reported that the villains would be Klingons. Of course with any rumor take it with a grain of salt.
badassdigest.com
I have an informant placed close to the production of JJ Abrams' Star Trek 2, and this informant got in touch with me to reveal that it looks like the storyline of the film has been decided. This person says that until the script is turned in anything could change.
Some sources give you all sorts of info, but this source likes to play games. I couldn’t get the exact character from them, but I got an email that reads:
It’s definitely a character that will make fans of TOS excited. 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.

Helmsman Mitchell and ship's psychiatrist Dr. Elizabeth Dehner are both knocked unconscious by the barrier's effect. When he awakens, Mitchell's eyes glow silver, and he begins to display remarkable psionics.
Mitchell becomes increasingly hostile toward the rest of the crew, declaring that he has become godlike, enforcing his desires with fearsome displays of telepathic and telekinetic. Science Officer Spock (Leonard Nimoy) comes to believe that Valiant crew members may have experienced the same phenomenon, and others must have destroyed the ship to keep the power from spreading. He advises Kirk that Mitchell may have to be killed before his powers develop further, but Kirk angrily disagrees. - Wikipedia

Harry Mudd - A human conman, rogue and trader/smuggler of the 23rd century who fled into galactic escapades to escape his shrewish wife Stella.
In 2366, James T. Kirk helped send Mudd to a rehab colony after he was caught using the illegal Venus drug to beautify three women he hoped to sell to miners on Ophiucus VI as brides.
Mudd's offenses at that time had included smuggling, transport of stolen goods, and purchase of a space vessel with counterfeit currency. - startrek.com

Talosians were once a technologically advanced culture but a nuclear holocaust left their planet virtually uninhabitable and killed most of the species. The survivors of the nuclear war congregated in underground dwellings, where they became dependent on their mental ability to create stunningly real illusions, an ability that had been developed by their ancestors. As their mental powers grew, they lost the ability to use the technology left behind by their ancestors. The Talosians found that life using illusion was addictive, almost like a Human developing a physical and psychological dependence on narcotics. They became bored with the content of the illusions which they had. Their dependence upon these illusions for mental stimuli caused the Talosians to begin capturing space travelers to use as the living basis for their illusions.- en.memory-alpha.org

The U.S.S. Enterprise must cross an empty sector of space on their way to deliver supplies to colony Beta VI. In this space, they find an uncharted planet whose presence can't be explained.
Trelane, a humanoid with tremendous psionic powers and a passion for Earth's 18th-century military history. It is he, they discover, who impulsively kidnapped Kirk and Sulu, wanting to add them to his arena of the Napoleonic era that he has created on this planet, Gothos.
While Trelane has great powers, he has little self-control and is spoiled, willful and impetuous. When McCoy and Jaeger appear, Trelane invites them all to join him at his party.- startrek.com

The Horta is a highly intelligent, silicon-based species, that is capable of tunneling through solid rock ike humans are able to walk through air.
Discovered on the planet Janus IV, the Horta is female, and lives below the planet's Federation mining facility.
Around stardate 3196.1, the Janus VI miners were suddenly attacked repeatedly by this creature, who as it turns out, was merely trying to protect her eggs. The miners were unaware that their mining posed a serious threat to both the Horta's unborn children and to the future of the entire Horta species.- startrek.com