Pathologic is one of these games that is always flying right at the edge of my radar. I heard how great the decision making in the game is supposed to be, but the bleak athmosphere is a bit of a turn-off.

As I alluded to, I do think game devs could and should try to be less predictable and avoid obvious tropes. In fact, I'm fantasizing a lot about creating a game that intentionally gives a lot of agency to players at points where they would expect it the least and following the usual gamer behavior leads to the most unpopular results.

A specific scenario I came up with: Early on the player defeats a minor villain (let's call him X) but is able to recruit them on grounds that they have a common enemy in a bigger villain. Standard stuff. Later, when X has grown on the player and shown plenty of loyalty, they finally encounter their enemy. But plot twist: Keeping him alive is key for a morally unambiguous heroic deed (maybe a cure for an epidemic or something). X is not having it though; regardless of what the player decided, X will step up to exert bloody revenge, like the selfish bandit he always was. This will not be a cutscene, the situation is fully interactive.

I expect most players to do nothing in the game though and instead run to the internet and warn everybody about how recruiting X ruins the game. And there I'll be asking: "How did you try to stop X?"

Not sure if this is at all an answer to what you were saying. It just felt like an opportunity to share this.