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.
Actually by giving these points, you've proven that it wouldn't be awkward or bad at all to have him not be Khan. For example:
1) Kirk and Spock's reverse death scene from TWOK is indeed a very obvious (quite literally copy-pasted) homage that would be apparent to anyone who had seen the original. That entire sequence needs no changing and actually would've fit better as an homage to TWOK without it actually having to be a copy-paste that doesn't even fit in its current state. The death scene might even have had more significance because people who have no idea what TWOK was would see it for the first time in a unique context.
2) The only difference in Khan's people would've been their origin story which is about 1-2 sentences worth of explanation in a dialogue placed early in the movie's setup phase. In fact they would just have to change the number of people created to make Section 31 look even more diabolical and "outside Starfleet's morals" in a way.
3) Honestly the phonecall to Spock is probably a scene that should've been done away with anyways. It makes absolutely no sense that the current Spock can just call up old Spock for everything the Enterprise runs into. The Temporal Prime directive apparently isn't important to Spock anymore and destroys every ideal surrounding Starfleet's handling of temporal anomalies. How are these officers supposed to grow up and become competent if they are literally given everything and learn/cope with nothing?
The way I see it, dancing around Khan without actually being Khan is a true homage and not a poor copy-paste job that we got instead. Homages are meant to be subtle. It also would've lent to the idea that the adamant defenders of Nu-Trek have always maintained; that Nu-Trek is an alternate timeline with similarities to the original without being a bad attempt at copying the original. If you're going to be another universe, make it another universe with unique villains or its not a reboot, its a bad copy. The new timeline has so much potential if it tries to break itself away from the original. It has little to none if it continues on this road.