This is a difficult question to ask considering you need to use motive and evil deeds to back up your reasoning... If we're asking who is truly evil then only one villain technically fulfills that and its Ex-Death from V.
Considering he's a sacred tree corrupted by evil human magic sealed within him; he's the only villain in the series that can be said his personality is truly evil cause its all he's ever been and known. As villains go, he lacks any real motive. He's evil cause he is evil.
Chaos fought for destiny and revenge
Palamecian Emperor fought for personal glory and power
Xande feared death and the Cloud of Darkness is a force of nature and beyond morality
Zemus was a racist but little is known of his other traits and status but it could be speculated that he was noble to his own kind before they sealed him away for suggesting genocide. Zeromus is an incarnation of Zemus' hatred and is the only other villain I might consider but then again from his perspective he was betrayed by all...
Kefka was driven insaned by experiments done to him but it doesn't change the fact he's the series only sociopath... I'll get to this later...
Sephiroth is driven insane by the truth and eventually gets it in his head that becoming a god is his birthright cause he's trying to fulfill the nature of Jenova that exists in his genes. Even then, his acts of cruelty are done more out of necessity than personal malice. Granted this changed when KH and AC came out but KH Sephiroth is not canon and AC Sephiroth is not the real Sephiroth in my opinion so neither count. All signs of Sephiroth being a cruel bastard are a result of Cloud's messed up little head.
Ultemacia is only tossed to the side line cause she was so poorly developed. her motive is illogical and her means to fulfill them even more so. She's just bat-crazy and nothing more...
Kuja has the most sympathetic motive of all the villains except for maybe Xande but his means of doing it are clearly evil and villainous...
Sin is just stuck in a personal loop of his final thoughts before death and can almost be considered a force of nature. Seymore is the same as Ultemacia.
Only played five minutes of XI (curse you crappy internet connection!)
Vayne has personal glory in mind but is also thinking like a ruler so his motives are not clearly evil though it is underhanded that he gains alot for his efforts...
Now this is my feelings if we look at this for face value and not from a psychological or moral level. In that case, Ex-death is still a contender but Kuja and Kefka once again become contenders. All three villains truly do some heinous actions but more importantly... all three share the common trait of enjoying their evil acts. The other villains either didn't care or justified it in a twisted sense of morality.
Of these three, Ex-Death is a result of human mistakes. A physical embodiment of man's desire to destroy themselves (evil and forbidden magic) and the world around them (using sacred trees to seal their mistakes). Ex-Death destroys and kills cause its his nature. He literally is an embodiment of evil and his actions are taken straight from the pages of human history and depravity.
Kuja has a motive of seeking freedom but lets face it, he has to reduce the entire world in ruin just to get enough power to do it and when its all said and done, he decides to annihilate exhistence cause he can't fathom the world going on without him. So better for it to die with him. Its difficult to not judge Kuja's evil without seeing what he did. Granted a few villains before him attempted similiar feats in games prior to gain something but he's one of the few who accomplished his initial goal and can be thought to have actually devastated the world to do it.
Kefka gets some special props as well but I feel Mercen-X said it best. I think Kefka gets special props cause he's one of the few human villains who actually turned his back on humanity. Most will say he's crazy and he is cause he's a damn sociopath. The closest thing human psychology has to a definition for evil. The other villains except for Ex-Death could be thought to have some admirable traits if viewed from the proper light but Kefka has none. He will kill without hesitation and doesn't give a damn who you are. He posseses the terrifying trait of immunity towards reason and common morality. But the real clencher I feel is that he is human and still has these traits. Even more terrifying is that you watch his mind regress as the story goes until he thinks of himself as a god who's judgement is absolute. Even more than Ex-Death, Kefka enjoys killing and spreading chaos. He lives for it.
With the above statemants, I feel Kefka is the most evil cause Kuja and Ex-Death have stronger justifications for their actions than Kefka does and Kefka out of all the FF villains really enjoyed what he did.
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