*The nuTrek creators (except for Abrams) are avid Trek fans (most of the series)
*They enjoy putting in "Easter eggs" and other homages (Tribbles, Admiral Archer's prize beagle in the first film)
*Cumberbatch's villain is A) wearing a Starfleet uniform and B) can withstand being hit by Spock...HARD...as well the Vulcan nerve pinch.
*This movie's scale has been touted as being much more expansive than the previous movie.
So I take that info and interpret it to mean not Khan, not Gary Mitchell, but...
He's wearing a Starfleet uniform because he's posing as a human being and wants to manipulate the crew of the Enterprise.
And Trelane wearing a Starfleet uniform would be a nice homage to Q's frequent donning of Starfleet uniforms.
I'm going with my theory until proven otherwise...