I thought Star Trek Into Darkness worked pretty well for something inside the Star Trek universe.
The reboot established that this was a world in which the events of TOS, the films, etc. did not necessarily apply. At the same time, this is Star Trek, so certain facts (e.g. Klingons, transporters) are part of a persistent universe—a world in which the eugenics wars and the Botany Bay are part of a preestablished timeline.
In this timeline, the Botany Bay is discovered early, by Admiral Marcus, who has certain militaristic intentions. He thaws out the Khansicle, and instead of stranding Khan as TOS Kirk did, he uses Khan’s cohorts as ransom for Khan to develop weapons.
Khan escapes, Marcus covers up his own malfeasance, and Khan swears revenge. Kirk unwittingly gets in the middle of a bigger plot between two egos more powerful than even his own, and learns a lesson about self-sacrifice and the futility of vengeance.
In a persistent universe, Khan would have to exist, and would, at some point, be discovered. Getting Star Trek’s most iconic villain established would have to happen eventually, in much the same way as Batman will eventually be forced to meet the Joker, Spider-Man will eventually have to face some iteration of the Green Goblin, and Dr. Who is gonna be running from some Daleks.
As such, Abrams and company did an admirable job not completely screwing up the character.
You CAN take issue with the pure fanboy throwback to Wrath of Khan inside the warp core. I prefer to look at it as a Groundhog-Day-esque replaying of predestined events in a universe where a butterfly flapped its wings a little too close to Vulcan in the series reboot, but that’s just my take.
I still have my Flickr pro account.