My favorite villain would be Kuja. Yes, he's narcissistic, cruel and obsessed with power but he's also shown a side that's not common with many villains a good side you might say. Also he's proven that even a villain can be a perfect gentleman and unlike many villains he did regret for his evil deeds.

Also Kazuya Mishima is one of my favorite villains, well, if you can call him a villain. From a innocent kid to a young man raging with anger and obsession for revenge which lead him to his own misfortune. And because of his selfish personality he's turned against his own legacy and everything that was important to him.