I like how people always forget that this film was advertised with John Harrison. Khan was a secret and surprise. People went in to see Kirk & Co go against Benedict Cumberbatch who delivers deep voiced monologues while looking menacing.
The point being? The name of the villain was completely irrelevant. It could have been Soran, it could have been Khan, it could have been John Doe, it could have been John Harrison.
All those "the audience doesn't care for a villain unless its Khan" arguments are nonsense.