Am I alone in thinking the villain's outfit has "Section 31" written all over it? The all-black leather, the squared off shoulders - it's totally the same design aesthetic we saw on DS9 and Enterprise when an agent of Section 31 was on the scene. I think that bodes well for the film, as the idea of a shadowy, top-secret intelligence/defense agency that exists in the heart of the Federation and that is above accountability seems like it is ripe for dramatic conflict. I loved that this agency was introduced in DS9, as it was in keeping with the darker tone of that show, but I felt that the idea wasn't explored to it's fullest potential, due to the show's run coming to a close at the end of season 7. It's great that they revisited the idea on Enterprise, but again, that show was cut short before they could do much with Section 31. I'm hoping Section 31 is rearing it's ugly head again in the time of Kirk and company!
If that is the case, perhaps the best way to ID the villain is to consider which TOS-era character is most likely to be a secret agent for the dark side of the Federation?