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.