I don't think Kuja's necessarily evil. Some part of his concience actually lit up at the end, whereas you got players like Kefka who seriously don't give a sh*t if the world's destroyed, as long as he's in power with the ultimate power and stuff like that.
As compared to Necron, necron seems to be the theory of all evil. true he's like a total noob to people who want to beat him (Ultimecia was much harder than him), but it all depends on what you think is worse. Somebody who wants to end all life or make mankind slaves? If necron's pure existance is to end life, he'd end himself too. Does he not care? Is he nothing more than a machine? Therefore is it safe to say he's evil or just some droid designed to (attempt) destroy all life when the time is right?
To beat Necron btw, be fast, heal lots, and use Dispel and Regen.