The REAL bad guy (girl?) of Star Trek Into Darkness is someone we haven't met yet, someone the prerelease marketing isn't even hinting at.
If you consider the original draft treatment for STII, what we know about this movie fits quite well into context (it's been posted elsewhere here, but I'll paraphrase). The idea is Kirk et al. are sent to quell a rebellion on a Federation colony, only to find that the rebellion is being led by his son David. As it turns out, Khan is the mastermind behind the scenes.
So, substitute John Harrison for David Marcus, and voila. Star Trek Into Darkness.
Also, long before we had Khan, the villain was supposed to be Harold Ericsson, a nordic "superman". As someone else pointed out: HARold erIcSSON = HARRISON.