Khan was a very different character, Carol was a very different character. How they interacted and met was very different. Khan's goals were very different, etc. There was ONE scene that I thought went too far with TWOK references, but that was near the end of the movie. STID is different from TWOK, period. Also, the point of a reboot is to both do new things, but also take old concepts and put new spins on them, which this film did. Saying that JJ can't use Khan is like saying that a Batman reboot can never use the Joker, or a Superman one can never use Lex Luthor, or a Spider Man one can never use the Green Goblin, even if they do different things with those characters. That argument is absurd.