They treated the whole Khan thing way too comic book like. Khan is not the Joker, who is a constant enemy of Batman. Khan is just one of many antagonists, and the crew had to face a lot more problems and adventures.
They confronted V'Ger, the Whale Probe and stopped a Klingon-Federation conspiracy. All that was far more dangerous than Khan ever could haved dreamed of being.
And yet none of the others managed to inflict the damage (physical and emotional) that Khan did. I'd say Spock isn't wrong on this.
Not necessarily true:
* Kruge ordered the death of David, and left Kirk embittered for years to come.
* Chang gutted the Enterprise worse than Khan did: blowing a hole clean through the saucer. Framed Kirk for assassination, and was nearly successful in starting an interstellar war.
* Soren killed Kirk, trashed a planet, and his actions lead to the destruction of the D
* The Borg Queen nearly rewrote history, screwed with Picard's emotions, and assimilated an unknown number of his crew.
* Shinzon led to the E being nearly totaled, the mental rape of Troi, the death of Data, and screwed with Picard's perception of himself.
Plenty of others have ranked up a equal to higher tally than Khan. Khan's rep is largely post-TWOK hype centered on Spock's death. The Boba Fett effect.