So we would have had a man with superior abilities, who is out for revenge against a Starfleet admiral and his followers who also have superior abilities who are in cryo-storage for the most part.
So this doesn't sound remotely similar to an already existing trek villain?
That was essentially my conclusion. I was initially disappointed they'd used Khan instead of a new villain, but I liked the story otherwise and I couldn't come up with a new villain who fit the story and wasn't so close to Khan as to be an obvious copy - in which case IMO it's better to be up front about it and have him be Khan.