Eh, I wouldn't regard Necron as the villain of FFIX. As someone said, Necron was like a last ditch effort of Kuja. Necron would be the last minute villain if he was like responsible for everything or if Kuja was Necron's subordinate or something like that, which isn't the case. Kuja's still the villain, Necron's simply the final boss.

Anyways, I was about to make a list and I realize the only villains I actually liked were Kefka and Kuja. Others were either underdeveloped or underwhelming or just plain out stupid (*coughgenesiscough*), and Kefka and Kuja seemed like the two exceptions. So, I'm just going to leave it at that.