Khan is such a great villain because he is quite rational. Nothing against the later part of TWOK but when he is consumed by his desire for revenge (and Joachim tries to calmly tries to convince him of what would be best for the Augments) he becomes a bit of a joke. Same with Malik wanting to eradicate a Klingon colony in The Augments. TWOK does not work because of but in spite of Khan going crazy.
But rewriting the past of Khan and making Frankenstein's monster into Frankenstein himself is plain stupid. It also wasn't necessary, being a tyrant is already evil enough. But I guess they just had to make him into an always genocidal super-uber-evil villain.
It's kinda like with Dukat in DS9, somehow the folks in charge could not resist retarding a complex character into some stupid one-dimensional incarnation of evil. I always liked the Trek stories which said that evil is among us and not out there. Most eugenic stories, be it Savage Curtain or Farpoint, clearly emphasized that humankind was the bad guy and not its creations.