Again, Khan is a character, not a story. Him being brought back is no different to Moriarty in various Sherlock Holmes adaptations. Joaquin Phoenix may be Lex Luthor in the Man of Steel sequel - is that due to a lack of ideas or simply them using the Superman mythology?
I don't think Khan is comparable to these recurring villains. He was a one-off who just happened to get a movie. He's not the Joker.
That's only because Trek hasn't been rebooted before. Khan, as villain of Trek's most popular (and, arguably, most important) movie, is an obvious choice to resurrect.
Khan got a three-episode tribute in Enterprise (where they even replicated Khan's death by having an injured Malik crawl across the bridge to the self-destruct controls) and at least 3 novels detailing his backstory.
Now if it were Mudd, then that would be different because he was that type of villain. A movie with Mudd would be boring though, and using him as a character isn't the same as using Khan.
He got a mention at least. And a cool little ship.