Why does anyone assume a movie with Khan as the villain has anything to do with TWOK?
Tim Burton made a Batman
movie featuring the Joker. Big success. Many years later Nolan made another. What did the movies have in common? Not much.
Khan is by far the best-known antagonist in Star Trek
to the general audience. That is reason enough to use him. That said, TWOK was far from the most interesting story that can be constructed around such a character.