FFXII and FFT definitely had the most complex villains. Kefka was also great just because of how much he owned it, but definitely not that complex. I think the 'MUAHAHAHA' villain is an issue with RPGs and fantasy stories in general. I do appreciate a villain that is not just out to destroy or conquer everything but just make it better for their side or their ideals, and the player just happens to be on the other side of it.

I also appreciate Lavos as a villain. Definitely a 'destroy everything' type but not evil or malicious. Just a parasite doing what is in its nature. There is something interesting about that group going up against something with no feelings or wishes, just instinct.