Frostflare, Ultimecia had an awesome character design, but....that whole plot felt a bit rushed. As far as we know, Ultimecia had virtually no backstory -- at least, none that were mentioned in game -- so we have no ideas about her motivations. If we had some hint as to -why- she really wanted to compress time and/or what caused her to become the villain she was in the game, I would've felt more of a connection to her.
St. Ajora from FFT is my favorite xD Followed by Yevon, though I'm a bit confused about that too (mostly because it's been ages and I never actually finished the last boss). From what I can tell 'Yevon' was never meaning a god, anyway, but the church and the teachings they created. It wasn't until my second playthrough that I realized when they -said- Yevon, they literally meant the religion. So the endgame tick-Yevon is probably more a representation of the corruption within the church than an actual deity. Though...there's some inconsistencies there, too....I really need to play it again :< That'll help me write for Nadani, too~