I remain firm that I feel the villain is Khan.
1) At :20 in to the video (the one I saw), you see the villain swinging a rather large object but has the stature and features of a normal man. Khan and his ilk had super-human strength,
up to five times stronger, even being stronger than Vulcans who are known to be up to
three times stronger than humans.
2) "For I have returned" - Khan was the leader during the Eugenics War in the 1990s and was subsequently released from hyper sleep by the crew of the USS Enterprise ~200 years later.
3) "To have my vengeance" - There are very few characters in the early Star Trek universe who are so blindly lead through vengeance, revenge or wrath. This man once held an 'empire' which had a fourth of Earth covered. Once the Eugenic Wars ended, most of his kin were executed while the rest escaped on the USS Botany Bay and this might be the direction his new-found vengeance is based on.
4) "For your family" - in the extended Japanese trailer, he makes this comment. Khan and those like him were known as the "Children of Chrysalis".
5) "A comforting lie told to protect you" - Khan represents a superior being in strength and intelligence. He is the embodiment of Friedrich Nietzsche's idea of the overman but, in spite of these improvements, still lead to great conflict and ownership of land and people. Perhaps the lie is to believe that as we evolve to become stronger and more intelligent, we would have no desire to pursuit such primal feelings. Khan is the opposite of this and often has much more intense emotion towards certain evens.
6) Kirk and Spock with their hands on the glass. An obvious nod but I feel this is a red herring as it would make the whole 'mystery' moot.
That's just my theory though. Even if it is Khan, we're still in an alternate timeline so trying to pin down exactly what happens until watching it based on previous information is thrown out the window.