Devon beat me to this one but I had already come up with it on my own.
Given the writers' well-known familiarity with Trek literature, I wouldn't be surprised if Greg Cox's "Eugenics Wars" duology provided some inspiration for the next movie. Those books chronicle the "Rise and Fall of Khan Noonien Singh" from the early '70s through 1996. Early on, Gary Seven actually served as a mentor and guiding influence to Khan, trying to restrain his instinct for world conquest, but ultimately Khan would not be tamed. Seven was the one who eventually thwarted his grandiose plans and drove him off Earth entirely aboard an experimental DY-100 sleeper ship.
My money is on Peter Weller as Gary Seven. Do a Google search for Weller and Robert Lansing (who originally played Seven) and compare the two side-by-side. I'm betting that either the first part of the next movie takes place in the 1990s to establish Khan's origins, or Seven somehow winds up traveling into the future--or simply lives that long--to help confront him when he's rediscovered.
All of this is assuming, of course, that the rumors about the main villain actually being Khan are true.