...if he was a bit more patient? TOS' "Space Seed" depicted a Khan Noonien Singh as "brilliant", but his arrogance proved to be his downfall. He should have bid his time to make his move. Or better yet, just petition the Feds for clemency, then set up shop on a colony if he was to opposed to integrating with normal society. Maybe if Khan was not such an ego-maniac, he could have used his brilliance to re-direct the Federation into something he could control. BONUS: What if Khan turned good? Meaning, based on pure altruism, what could Khan do to make humanity, and this the Federation, better? How would the TNG era turn out?
I don't know what Khan would have done with a Starship, but it probably wouldn't have been much more than he ended up with -- a planet at his disposal. If Khan had been good, that'd be interesting. He was a superman, but not qualitatively more than human (and no more super than, say, Mr. Spock -- who comes from an entire race of such superbeings). The question is what Singh did besides rule. Was he a scientist? A gardener? An avid philatelist? Otherwise, he just becomes a conspicuously talented COO for a 23rd Century corporation...
All I know is that if Spock hadn't illogically countermanded Scotty, Khan wouldn't have come as close as he did to totaling the ship.