I much prefer the idea of Trek's version of the 90's being a secret history, as told in Greg Cox's Eugenics Wars: The Rise and Fall of Khan Noonien Singh
novel duology, the details of which only becoming public knowledge sometime post-WWIII.
Trek writer Roberto Orci is a fan of those novels, so if Khan does crop up in Star Trek Into Darkness
or Star Trek XIII
, they may base his backstory on the one in those books (similarly to how their George Kirk was loosely based on the version in Diane Carey's Final Frontier
and Best Destiny