"Clearly acknowledged now as a lost opportunity" by a vocal minority of self-described hardcore Star Trek fans, perhaps. In a more general way, I don't think so.
Abrams seems to think so, hence referring to the way it was handled as a "mistake". That's from the horse's mouth, not just some vocal minority of self-described hardcore Star Trek fans. I agree with him. Had they been clear it was Khan from the get go, there would have been more hype and publicity over the fact that Benedict Cumberbatch was going to play an iconic villain such as Khan, certainly more than "Cumberbatch will play some guy named John Harrison who terrorizes Starfleet and such". Best case scenario, many folks unfamiliar with Khan would actually be interested in checking out the two stories with Khan, and even better, like them enough to really look forward to the next Trek. Isn't that what all fans want, for everyone to enjoy this franchise we all love?