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.
You seem to equate killing more people with being a better villain, which I don't understand.
You have to look at Khan's actions and compare them more to a person who hit the lottery. Most people when they hit that jackpot dive in and don't think about tomorrow. Khan had been stewing in Hell for fifteen years, then he got a shot at payback at the person who put him there.
Khan's actions aren't rational, but they are predictable for someone whose been in that situation.
The Genesis Device is a plot device used to up the urgency of our heroes engaging Khan (the number of people killed doesn't matter, it's that the threat exists). It keeps Kirk from disengaging and warning Starfleet. It serves the exact same purpose as Thalaron radiation and Red Matter.
Again, there's a reason why The Wrath of Khan
has been used as a template for Trek films multiple times... because it is the "cream of the crop". I may watch other Trek films more, but if I'm introducing someone to the Trek films... it's the one I go with. Think about how simple the concept is, "bad guy with a big gun has an axe to grind". It was copied in both Nemesis
and Star Trek 2009
and arguably in First Contact
. Yet, in none of these films does the villain come off as sympathetic as Khan. Khan has an actual score to settle, he was wronged by Kirk.