Up until now, I've never realized how few villains in FF are actually sympathetic. In fact, the most sympathetic ones are probably Shuyin and Caius from the sequels to X and XIII.

I can't sympathize with Exdeath, Kefka, Sephiroth, Ultimecia, Kuja or Barthandelus. From what I've heard, it doesn't seem like Garland, Mateus or Xande are sympathetic either. Seymour and Vayne are debatable. Seymour tried to eliminate suffering from the world, just like the party - it's just that he is very, very misguided and thinks that mass genocide is a proper way of doing it. Considering how much stronger he himself got when he died, no wonder he thought he was doing something good when he wanted to kill everyone. Vayne is kind of like "ends justify the means". He's kind of like the main party of XIII in his motivation, but his methods are what makes him unsympathetic.

Shuyin and Caius are both "if she can't live, no one can" in some form or another. Not really sympathetic either, but probably the most out of them all.