Into Darkness was about terrorism and drone warfare and growing up and paranoia and etc. Didn't you see those apparent themes?
It's hard to see a theme when all you have are random story elements stuck into a flimsy framework to set up and connect action scenes.
Action scenes like....
*Kirk and Spock discussing the ethics and legality of their mission
*Scotty and Keenser resigning over their mission
*Kirk deciding to capture Harrison alive for trial rather than execute him with the long range missiles