Focusing only on the villain. I'll compare Khan and his actions and motivations to the comparable villains of the other Trek films. They being First Contact, Nemesis and XI
Khan was there first. All the other films you mention were trying to copy The Wrath of Khan
to various degrees. Behind-the-scenes people on Nemesis
were even calling it their "Wrath of Khan".
Remember the old saying: Imitation is the sincerest form of flattery
Nice proverb. However given Khan's feats and later feats of the villains I mentioned, I don't think we should hold Khan above the rest like he's special. Actions matter and Khan doesn't have the record to run on as the supreme villain of the Trek film franchise. He's not a Darth Vader level character. Vader who in Ep. IV and V showed himself to be strong, cunning, expert pilot, ruthless even toward his own men, and without mercy. Khan is more like Darth Maul. A glorified one shot villain who's only claim of success is killing a main character. Maul killed Qui-gon and Khan's actions killed Spock.