Lady Mjrn
Viera of the Wood
Again, I turn your attention to Kuja, who I personally believe should be a rolemodel for RPG Villains everywhere. Kuja was...a meanie. He was bad to the bone and he made sure you knew it. This was a man who would manipulate, destroy, and torture to get what he wanted. Yet, at the same time, he had motivation that we were made aware of. While he was certainly a terrible human, he was still human (well, technically, he was an Angel of Death, but you get where I'm going with this). You hated Kuja, but at the same time, you could sympathize with his plight, as well. He had a genuinely 3-Dimensional character that actually required thought to fully understand.
I completely, 100% agree with everything you said here. <3 Sums my opinions up very well.