Hey, some of us haven't quite beat X here
Anyways, for me, Kuja and Kefka are honestly the only main villains I liked. Kuja had a motive and was largely developed, so you could empathize with him. Most of the other villains (Ultimecia, Garland, and Ex-Deaths to name a few) just never had that development. Kefka is just plain crazy, and I like that.
As far as secondary villains go? Well, we have Cid from Final Fantasy XII, another crazy pal of ours. There was also Gilgamesh from FFV, who was just plain awesomeBut that's about it really. Honestly, villains haven't exactly been the series' strong point. Its more of, he's EV1lL and you must stop him.