In general, I think we may be confusing "plot device" with "plot." Again, "Moriarity" is a plot device. The Hound of the Baskervilles
is a plot.
Along the same lines, "superhuman villain from the past" is a plot element. It's not a story.
I got three new stories out of Khan. The new movie invented another one, involving Section 31, the Klingons, terrorism, conspiracies, etc. It's not like they just recycled the script and "rearranged" the scenes from "Space Seed."
(Does the movie borrow a single scene from "Space Seed"? I can't think of one.)
And the new comic books will presumably find something else to do with the character.