And if that was the change then, as I indicated earlier, I might have been left thinking, "Geeze, why not just make him Khan instead of BSing around the fact that that's basically who he is anyway?"
Besides, it would be -awful- if that was all they changed. Off the top of my head:
1) Kirk's death scene is an obvious homage to TWoK. If you're going to take away Khan, that entire sequence needs to be tossed out or significantly reworked.
2) His followers/family/what-not. It's too obvious a callback to Khan to have them and not have him be who he is. It might be workable with a much smaller number...or alternately a much -larger- number...perhaps Marcus was experimenting on a planetary scale.
3) The phonecall to Spock makes no sense at all if the adversary isn't someone we've seen before.
This is exactly why I said that I don't know whether the movie could have worked if Khan wasn't the villain...because the minute you want to have the villain not be Khan you cause a ripple effect through the rest of the film, unless you want it to be obvious who he's supposed to be.