Vanye Carudas Solidor from FFXII, that one game everyone hates.
Although its debatable if he is a villain since the game calls him a villain and the heroes are the group that are gathering WMDs to wage a meaningless war, in fact the heroes and the villain never confront each other until the very end because Vayne has better things to do than baby sitting a selfish warmonger princess. He has empire to do that for him while he focuses on freeing humanity and the other races that lives in Ivalice from the control of conceited "gods", Vayne doesn't discriminate between humans and pig people.
Vayne doesn't always do things that one would consider noble, he is still a villain, but only as much of a villain as Lelouch. He eliminates anyone who stands in his way from succeeding the throne because all the other characters only think of what's good for them, he on the other hand is more concerned about humanity's future. He offers Ashe the position of princess of the land which her kingdom rightfully lost after losing a long fought war just to avoid meaningless bloodshed, in fact most of Ashe's soldiers have joined with the empire while Ashe was hiding in the sewers and performing petty acts of terrorism against the empire like blowing out their plumbing.
Vayne's ultimate goal is to break the control the Occuria have over humanity, which are some godlike entities who have controlled the course of humanity throughout history. Ashe's kingdom only existed because the Occuria used one of her ancestors as a pawn and given him WMDs and Eldritch Abominations to control and take over the land. He does work with Venat, who is the renegade Occuria, who is meant to symbolize chaos but that's just because the Occuria believes that without their dominion over Ivalice the populace will bring about their own destruction, they probably will if they put Ashe in charge.
Even in the end when Reddas has destroyed the Sun Cryst, therefore fulfilling Vayne's goals, both Venat and Vayne turn against the heroes and pretend to be seeking the destruction of Ivalice now. This is all a farce of course, so that both Ashe and Larsa can be considered heroes by defeating them and peace will be finally brought to Ivalice. Also both Vayne and Venat know that they have taken some highly questionable actions in order to reach their goals, they have no place to fit in the future they have created for Ivalice, actually now that I think about it Vayne is exactly like Lelouch.