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Ultimecia. Even though losing the aeons for the final battle was sad and all and the yevon-aeon music was AWESOME(!!!), Ultimecia's three forms + Griever and the The Extreme and the fact that the entire final battle sequence wouldn't require a maximum of 14 regular attacks when levelled up a little. And Ultimecia has a scheme, Yevon's just lost his mind entirely.
Although both of them are one the 'wtf last minute ultimate villian' list, I'd say Ultimecia. Partially because the Rinoa-Ultimecia theory, if true, is the only thing I like about Rinoa.
And because Yu Yevon is not even a character