6. Enemy Mine
Into Darkness was based around the idea that hundreds of Starfleet crew built the biggest ship in history and nobody noticed. This was of course ridiculous, but the idea of a mole inside Starfleet is an interesting one. Perhaps a Klingon sympathizer or undercover agent, perhaps some character that shows what humanity is like now and hold a mirror to society. This would have to be handled delicately or it would risk being a pantomime, but done properly it could help to show how greed and distrust can be overcome. Star Trek was always at its best when it reflected society in a post referential way, mocking our current barbarism and relative immaturity as a species. The expectation is that the 5 year mission will be well underway so there is plenty of scope for home-sick, fatigued, traumatised crew members to rebel against Starfleet. Perhaps an insurgency of peaceniks who feel that Star Fleet is nothing more than a military, empire building organization with vaguely communist overtones. Or, in a more human vein, perhaps a character who feels wronged by Kirks fast rise up the ranks, a jealous ex-classmate or previously superior officer intent on bringing him down. This may be too close to the Albert Finney story though, and one thing to be avoided in the next movie is the constant references to previous incarnations. Speaking of which