"It seems like the speculation that the villain in STID is Khan has been going on since before the movie was even planned. I have one question for those of you who still support this theory: WHY SHOULD IT BE HIM?"
It could be him, unless it is just a coincidence that the character, Harrison, was in Space Seed and shall be in STID. Another duo-point of suspiciousness: Abrams trickiness and the idea of Benecio Del Toro being the first choice for the villain (one who could actually swing the role effectively). I wouldn't put it past trickster Abrams to have hired Del Toro on the sly, getting Cumberback to humble himself for the good of the cause a la the eventual unveiling of the head-villian, yeah, Khan. His story need not be over in an alternate dimension--all that dismissive talk about how a new series of circumstances couldn't yield a great movie with Khan is more ridiculous than the proposition itself: that Khan shouldn't be thought of as the villian in STID.