The company who did "Pillars of Eternity", Obsidian, is doing a game titled "Tyranny", where the protagonist is supposed to be serving a "clearly evil" overlord, which will probably be characterized by having, to certain degrees, to be the bad guy.
The antagonistic characters in Order of the Stick are interesting, as with the above referred to "Tarquin & Nale" and that "vampire" was interesting for a long period, but they do have clearly good and evil deities, which means that choosing a side is less ambiguous and doesn't require faith in the sense we would use the term. The hobbit ranger "Belkar" trying to do good is also interesting, I suspect a lot of it is playing with the classic D&D alignment system.
I hope that Bioware makes some attempt to represent relativity and arguments and situations where using a relative interpretation is valid but also provides a defensible position for when taking a relative position is questionable. One of the best game concepts in Mass Effect 3 was "Indoctrination" and how pervasive and subtle it was, characters having perfectly valid and logical arguments for undertaking technological solutions and taking strategic positions that became increasingly untenable. It would have been nice if earlier in the series the players were positioned to take easier, alien technology solutions to get results that influenced the types of options available once the big bad was in play.