Many critics have mentioned having Khan as the villain was a mistake. [SNIP] And part of that could have been Khan, as well as many other things.
Using Khan wasn't necessarily a mistake, the way they went about it was. So they went with Khan because they feel he's Star Trek's ultimate villain. That's all fine and good, but then they kept it a secret, refusing to identify the villain for ten months after he was cast and then they told us his name was John Harrison.
If the reason they chose to use Khan was because he's the Ultimate Villain and the one fans wanted to see brought into the rebooted universe the most, shouldn't they have advertised that fact? Made it well known that? Not make it the plot twist of the movie and go to the most ridiculous lengths to keep it a secret.
Hell, I suspect someone must realize this in hindsight since the blurb on the back of the Blu-ray box says the villain is Khan in the second sentence.