I've been think about this since seeing the movie. From the time Khan is thawed by Marcus until the events of STiD, only a year has passed. Yet, somehow, in this time Khan is strongarmed into working for Section 31, given a lab job designing torpedoes, and possibly major systems in the Vengeance as well.
I have a hard time believing this all took place in a year. Although Kirk says "John Harrison" didn't exist until one year prior, can someone refresh my memory as to whether he said the Botany Bay was discovered a year earlier? It would make more sense for it to have been discovered MANY years ago. It would have probably made more sense for Section 31 to accelerate their programs after the Kelvin incident, and not the destruction of Vulcan.