The Xenogears/saga series had ethical-oriented villians:
http://xenosaga.wikia.com/wiki/Karellen - Very tragic EII anti-villian, you can easily tell from reading his quotes

and his beta counterpart from a similar game

http://xenosaga.wikia.com/wiki/Wilhelm - IEI

In spite of stereotypes, I feel EII's make excellent villains, albeit tragic.