Well the best Sympathetic villain I've seen is nox from the series wakfu. One of the reasons he was the best was cause he succeeded in committing genocide to achieve his goal being to obtain enough energy of creation (aka Wakfu) To go far back enough in time to stop himself from making a mistake that caused him to make him who he was. However upon succeeding he the amount all the wakfu he gathered only amounted to him traveling back 20 minutes after defeating the main character. The machine he used crumbles and the moment he traveled to was before genocide occured.
Nox was one of the most powerful characters in wakfu able to take on the dragons and eliatropes in wakfu. He himself is a xelor but for those who don't know what that is it means Time magi.
And the lore about dragons in the series is that dragons are always born with a sibling being a eliatrope. Eliatropes are physically human however can manipulate wakfu into portals. However the way they use their portals is a bit complex considering the main character who is an eliatrope learns to shoot a laser with them.
All together the series is pretty interesting. If you wish to watch the show the torrents for them are on brotherhoodoftofu.com
you should note that it is in french but has been englished subbed. If anyone wishes to learn more of the lore just ask.
P.S. nox was going crazy from the object of power he had and from feeding off wakfu to keep himself alive. Another note my picture I'm using is an Eliatrope
My flame shines bright. Just make sure not to get burned by it.