Sonak, you raise some interesting points about Soran, yet it's hard for me to agree fully because his goal/McGuffin was kind of strange and unfocused. If it was so impossible to get into the Nexus with just a ship, how could he have gotten into it the first time? And why not just take a few years to thrust a large asteroid into the Nexus's path instead of going through this rubegoldbergian process of blowing up stars? While his sheer, psychotic callousness in pursuit of a selfish yet almost romantic goal is interesting, it's just too big a case of overkill.
To me, the best Trek movie villain is Shinzon, because he's the only one who has a strong personal connection with the hero/captain. Khan has a personal vendetta against Kirk, true, but that's a fairly conventional hero-villain relationship, and it's undermined by the fact that we never actually see the two actors face each other directly. Kruge is a moustache-twirler without any connection or history with Kirk. Sybok has a history with Spock, and his character is pretty much the most worthwhile thing about the movie, but he's not really the film's villain, more a dupe of the ill-defined entity that's the real baddie. Chang is another Klingon warmonger, albeit a more charismatic one than Kruge. The Borg Queen does have a history with Picard, but again it's one of simple enmity, and she's really more an embodiment of a force of nature than a character. Ru'afo is just some guy with a grudge against some other guys.
But Shinzon is Jean-Luc Picard, a younger, twisted reflection of the same man. I find it intriguing to see them play off each other. There's a strong father-son vibe between them, as well as the philosophical question of whether a person's identity is predetermined by genetics or shaped by experience and choice. And although NEM is closely modeled on TWOK, it avoids that film's mistake, giving us several strong scenes between Patrick Stewart and Tom Hardy, letting them really play off one another. It's the most personal hero-villain relationship in any of the ten movies, and it's what makes the movie work for me despite its flaws.