Emperor Mateus vs Kuja

Well if we do go by achievements then Kuja would undoubtedly win. Not only was he literally the most powerful being in the entire two worlds, he destroyed one world and manipulated the other world into complete and utter chaos, nearly causing the destruction of the three major kingdoms, one which is mostly a repair job, the other has Garnet and the final one will take decades before it ever attains its former rank.
Mateus was never really all that...awe-inspiring...he was powerful, okay, he was undoubtedly ingenius...whatever, these are all aspects that Kuja also has, plus more.
Kuja was also a character you just couldn't help but like, from his smooth talking way, to the fact you hated how beautiful he was, to his horrible way of manipulation and even down to the truth behind all that he did. He was the only villain besides Seymour to actually grab the gamer in-game and made you feel something for him. At the end of FF9 you had two reactions for Kuja: You loved him and felt so bad for him, or you hated him.

With others, you really don't get such a connection with the villain.
Garland: You pretty much think he is a push over, then he surprises you (only villain besides Kefka and Kuja to accomplish what they wanted (Unless you count Kuja's true goal, then he's out)) only to yet again be bullied into submission. (I at least never found him all that powerful)

Mateus: Manipulative, powerful, ingenius and starts the trend of being more beautiful than he has a right to be, yet he doesn't really make a real appearance until near the end...also from the most tragic game of the entire series with a good deal of your teammates perishing or running off to do something else.

CoD: ...not really much to say on this one; I haven't yet beaten this game (Ipod Version)

I'm going to skip FFIV... no offense

X-Death: yeah...an evil tree...wow...and with the most generic of names to be thrown at us yet...I pretty much was disgusted by this guy the moment they told us his name...

Kefka: Ingenius, manipulative, and insane. He starts out pathetic and manipulates his way to supreme power, his life was the very essence of magic. You hated Kefka, you were annoyed by Kefka and you wanted Kefka to suffer. A villain that is seen throughout and one that you simply love to hate. Yet if you look into the depths of what he says and does, you notice tidbits of his sanity and care for Celes that seem oddly touching.

Sephiroth: I hold to my stance that I only ever liked Sephiroth, pre-crisis. He was cool, enigmatic, stern and overall a truly nice guy with a stoic demeaner. He was Sephiroth...then he goes ape-spit crazy and loses literally everything that was so awesome about him. He loses his true intelligence, lending more to his blind faith in fate. He literally devoted his plan to using a rock to summon a big rock to smash into a bigger rock. The only true thing people feel for Sephiroth in-game (once you discover the truth about his parentage) is this: pity. Nothing more, nothing less(well sometimes something less).

Ultimecia: As a villain the reaction is more along the lines of, "Who?" but in reality I slightly admire Ultimecia. Her way of doing things was unique to the series and well, she knew without a doubt that she would die and she still went down fighting. She was a villain who tried to stop the future and failed but knew of her demise and bravely fought against it. You don't feel much for her unless you think of it that way...

Kuja: Explained above but on a extended note, you realize if you play it through a second time that Kuja has a bully-syndrome where the way Garland treated him was the very same way he ended up treating the Black Mages and that everything he did was in order for him to find a way to simply live.

Seymour: the guy everyone loved to hate. You kill his corrupted @$$ once, then you have to do it an additional three more times. He has a lot of depth that really makes you feel sorry for the way he turned out. He literally grew up with a fostering hatred of those around him. People treated him horridly and his own mother was forced to do the only thing she could think of for her son; become a Fayth so that he could have the power to defend and help himself. All Seymour truly wanted was a peaceful end. One where there was no more hatred, no more resentment and no more pain. He may have gone about it in the entirely wrong way but you can slightly understand the conclusions he came to.

no offence but XII was crapola (imo)

Superpope: ...yeah...a guy with absolutely no depth and near zero visibility...like the game...he was a severe let down.
(on a side note, I can't wait til FFXIII-2 everything that was absolutely atrocious about the first one was changed for the supreme better in the second one (it looks to be an exceptional RPG))

not that this was entirely necessary but there you have it, take it as you will. lol