I agree: Khan is definitely NOT the Joker of the Star Trek universe
I disagree. His character brings it down to Earth and hits home more.
An interesting tidbit on Khans popularity per Wiki:
"The character has been positively received by critics and fans; Khan was voted as one of the TOP TEN GREATEST film villains of all time by the Online Film Critics Society."
The OFCS Top 100 Villains of All Time
1. Darth Vader (David Prowse/James Earl Jones, Star Wars, etc.)
2. Hannibal Lecter (Anthony Hopkins, The Silence of the Lambs, etc.)
3. Norman Bates (Anthony Perkins, Psycho, etc.)
4. Hans Gruber (Alan Rickman, Die Hard)
5. Frank Booth (Dennis Hopper, Blue Velvet)
6. Rev. Harry Powell (Robert Mitchum, The Night of the Hunter)
7. HAL 9000 (Douglas Rain [voice], 2001: A Space Odyssey)
8. The Wicked Witch of the West (Margaret Hamilton, The Wizard of Oz)
9. Graf Orlock (Max Schreck, Nosferatu)
10. Khan Noonien Singh (Ricardo Montalban, Star Trek II: The Wrath of Khan)
Khan even beats Nicholsons Joker in this one who was rated 16th at the time.
I think reintroducing Khan gives the writing team a chance to show some of Khans origins on film in flashbacks perhaps during the very interesting Eugenics Wars.
There is PLENTY that can be done with Khan that has not been shown in TOS (1967) and in WOK (1982) IMO.