Apologies if I'm rechurning what someone else has already said. I did read through the thread which prompted me to think about this but I may have not committed every comment to memory.
I guess my issue with villains in any game or story setting- PC or NPC- is that its such a binary concept. Good vs bad. Nice vs mean. Grace vs. evil.
And that's not wrong. But.
It's a concept that presumes that your character is in the default position of being in the right and the villain is the default position of being in the wrong. And their actions are supposed to be a staircase to your good PC achieving a state of grace through their act of evil.
And I want to be clear that I'm not knocking stories that have this sort of push/pull. There are people who want to unpack them for a number of very valid reasons. But the reason they're operating through this lens is because they're presented from a point of view that polarizes these actions that favors the 'good' because the intention is usually for good to win. The result is that triumphing actions are treated with virtue and the behavior of the villain is generally termed as having an antagonism. And I think we're conditioned to accept virtue on its merits even when there's little logic or actual supporting evidence that what's happening is actually good and the behavior of the villain is slanted for cause, wherein we're given within reach ideas about why this is bad.
I'd like to see the whole dynamic re-examined, I guess and step out of this frame work. So much of what we understand as conflict on a global scale is deemed as complicated and the argument about who is wrong vs. who is right is a thing steeped in relativism. That's definitely not the case in binary villain v. hero motifs most of the time and I wonder if purposefully framing it in the notion of who did what to whom is steeped in relativism would actually take the pressure off who needs to win.
