I'm wondering...
how Section 31 could have possibly convinced Khan to work for them. Khan does not seem like the type who would give in to threats of any kind. I've heard that S31 holds the other Augments as ransom, but Khan is also not particularly compassionate. Why would he care about them?
This has bothered me, too. Especially because the major flaws in the augments (as pointed out in "Space Seed") are that they are overly aggressive and overly ambitious. They can't help it.
He might care about them as loyal allies. He was the "least brutal" of the tyrants, remember. That said, I can't imagine how he would stoop as low as he apparently did for so long and not find a way to use his superior intellect and such to free them a lot sooner. How could someone who can't control his aggression and ambition be subservient to Starfleet for more than a day without being unable to take it any longer?