I feel like a lot of the Choice of Games that I’ve played here have a real issue with their villains. I think that a lot of them are just vaguely crazy and want to destroy the world to bring back their dead son, The Superlatives, The Lost Heir, and Heroes Rise all come to mind. And I think that some of the best villains in Choice of Games aren’t personal villains, they’re more just governments or organizations like the Hegemony in Choice of Rebels or the Antaris in Guns of Infinity. The only good personal villain I can think of is your nemesis in Mecha Ace, that’s it. These games are more about the main character and world than they are about a personal villain, but I thought it was interesting that are so often these cliches and was wondering if anyone knew about a Choice of Game that had a really good villain.
I’d name the M/Patriarch from Hero Unmasked!. Not so much for their motives but for how dark everything the respective character did and said before becomes when you think back. I think at one point I genuily growled ‘you fcking a-hole’ at my phone upon realizing the implications of an earlier thing.
The ‘villains’ are fairly complex in Orpheus Ruse, Metahuman Inc., and the two Deathless books, I think, partly because the choice of who is and who is not a villain is partially the players’.
I also liked the antagonists in Study in Steampunk, where there are definite motivations, though that game is gender-locked male.
A lot of the titles do seem to have more antagonists than villains, so the people you may or may not be working against aren’t necessarily bad, depending on the PC’s point of view—but they can certainly be working against your character.
Slammed! and Tin Star also have really solid antagonists, but who they are might depend on how you play (particularly in the latter), and I wouldn’t necessarily call all their antagonists villains, either.
Edit: @CorporalHam You might want to use spoiler tags when describing the motive and style of villainy in specific titles, in case people haven’t read them yet.
Agree with Fiogan, they’d be my pick as well for more complex villains and complex worlds 
(Out of the two Deathless books I’d recommend the first would be better for that if you’re tossing up between one of them)
I know I’ve said it before, but I really like orpheus ruse, definitely under rated. It’s a difficult one to explain but if you know anything about the government research into psychic abilities and then put a fantasy spin on it, that’s pretty close.
Metahuman is by the same author but more mainstream and does deal with a decent villain also.
Guess it depends on what kind of subjects interest you though.
You know both of them done by the same writer. 
That the think about war thier is one villain". For the most part you’re both individuals and conflict fighting for a fairly complex you political reason. The closest characters are or become villain to the ones you make during the conflict and can be on your own side.
Prince Mikhail of Khorobirit the strongest of the lord of Congress is less man of act and more like a force of nature.
I don’t really think of Khorobirit as the villain of that story though. He’s the opponent, sure.
But what about Elson or Carrecourt who gamble with the lives of common soldiers due to their hunt for glory and ineptitude respectively?
And what about Lefebvre, Lady Katherine and possibly the MC who are essentially war criminals?
Doesn’t this mass of villainy arraigned against him make Khorobirit the hero?
One of the things I kind of love about the series is everyone can be a justifiable Hero or monster. We could straight up commit war crimes in this game and have a fairly strong argument for the utility of are action. Where Mech Ace is a straight love letter to Gundam. In his infinite sea series it’s a Fantasy something that’s making commentary on both warfare and Geo political politics in the natures of Are choices. Is gaming in the stories enjoyable but it’s the anti-escapism and power fantasy see very common on the site.
It’s hard to develop a good villain with the story telling style typically used in COG games. The perspective is always from the protagonist in most games, so you don’t learn anything about the antagonist except when the protagonist interacts with them. A lot of COG games don’t even have a single major antagonist. Heroes Rise did… though she wasn’t really what I’d call good. The Demon Hunter series does, but he’s a literal demon so he doesn’t have the most interesting motivations.
Choice of Robots has fascinating antagonists, because while they often are organizations and governments, depending on the playthrough those antagonists can be the reason for all your suffering in one game and some of your most trusted allies in another. Once you’ve had both of those experiences, the antagonists feel so fleshed out that they genuinely seem real to me.
(I also really love the game, so I admit I may be kinda biased here)
I think for the best antagonist in a ChoiceScript game, though, I would give the prize to Slammed!. The writing in that game is awesome.
I have to agree with earlier posts about how hard it is to have good antagonists. That’s y in my WIP I have multiple and it depends on ur playthrough. Sometimes it’s outlaws, other times it’s the law and I will be putting faces to these factions so u know y they do what they do. And in every playthrough u will have to some how deal with the Apache and even have a conversation with Magnus Colorado and a young Geronimo
Now that I think of it, wasn’t Tierra the aggressor? And isn’t Antares absolutely casual about throwing massive hordes of their serfs against Tierra, in a horrific case of "We Have Reserves? And isn’t this entire thing being fought about what is, essentially, a religious dispute?
And isn’t the war basically going on for this long without major foreign intervention because the elves are planning to mop up whatever’s left, and stand to profit regardless of who wins?
That’s what I like about it so much: once you get past the veneer of honor, no one looks good.
Yeah, I think that some of the best stories don’t even have real personal villains, instead they have tragic circumstances that your character is just trying to survive.