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.
It would have been better if they had left when Khan was found and how long he'd been working for Starfleet vague.
According to Khan, it was the destruction of Vulcan that motivated Marcus and Section 31 to begin searching for the Botany Bay.
I imagine Spoiler: Section 31 Section 31 and Marcus had already been building the Vengeance and making their plans for years prior to discovering "Harrison", and then when they found him a year ago, they used his superior intellect to come up with ways of "tweeking" and improving upon the tactical systems they had already built - after all, look at how quickly Khan learned all about the original Enterprise, its defenses, etc in "Space Seed" by looking through the computer files - the man is a genius with an accelerated intellect programmed into him! I also think they probably used some sort of cosmetic surgery or alien techniques to alter his appearance to disguise his true origins!