I don't see why you wouldn't shout it from the rooftops that Khan is in your movie. If the bad guy were
somebody else from TOS then I could understand wanting to maintain some degree of keeping it seperate. But Khan is one of the franchises most iconic villains (for better or worse), heck he's one of the few villains that the wider public *would* recognize thanks to the "Khaaaaaaaannnnn!!!" soundbite entering popular culture.
From a marketing perspective, it really makes absolutely no sense
to pretend he isn't in the movie when he actually is.
Well, to be fair (I guess) - and there's a belated reply to JarodRussell
here - the script as writen very much encourages the hidden marketing and big reveal. If they'd advertised the "RETURN OF KHAN!!!" but only had our heroes learn his true identity halfway through, and at no point actually learn what made him such a fearsome figure in the first place, general audience and fan reaction would doubtless have been that the return of such a storied villain was a big ol' box o' nothing.
If, however, Khan had been the openly identified villain throughout the movie, it would have been impossible to keep that under wraps. It's only because the name Khan is such a small part of the story that they were able to do so - which in turn explains why it was so meaningless.