...and again, I'll say that if the only thing that changed was that he "wasn't Khan" but the rest of the movie remained essentially the same, I would have been left thinking, "If they're going to go this far, why not take it all the way and just say he's Khan?"
I -really- don't know what's so unclear about this.
"STID is about a genetically engineered supervillain from Earth's past who puts Kirk and Spock in a no-win scenario, and one of them must make a huge sacrifice to defeat him..." Really? Where have I heard that plot summary before?
Khan being from earth's past had nothing to do with the story.