Call of Cthulhu kinda dropped the ball with choices. I like the game, but I made an effort to save people, not harm them or not take the easy option and the cast don't ever really react or anything else. I'm pretty sure one of the cast even just kinda disappear from the game at one point, never to be mentioned again. Made the choices feel pretty silly.

I would say maybe Suikoden 2, since a lot of choices don't but then some of them change how the game ends in an unintuitive way.

Cave Story also has this problem except there you have no idea you even made a choice until later on.

Cave Story does have some rudeness, but I'd feel the choices are major.
Doesn't Cyberpunk also do the Bioware Iillusionary Choice?

Not sure what you mean, is this a mass effect reference, if so I haven’t played them (other than the first for a bit). DA: origins has back stories you actually play through.

I remember being really pissed off when after trying for a good long while I managed to escape that ambush early on in the first Deus Ex, only to discover that it's not really an option and there's no way to continue the game without getting defeated there. I guess I can't really blame the game, it's not like it gave me a choice and then ignored it, it was my own stupid tenacity that made me decide "no, there has to be a way out". I'm still kinda proud I managed it, even if it leads to nothing.

There's a few poorly designed instances of this sort of thing:
* One boss in Dragon Warrior 7 who doesn't seem to be especially dangerous (I think having the enemy use spells like Explodet was supposed to be a clue, but this is at a point where you can survive, and could realistically have the means to recover from it), but yet that particular boss has 65535 HP or so and you are meant to lose that fight.
* Lufia: The Legend Returns has one boss fight you're meant to lose, but which isn't that difficult. Fortunately, in that game, if you manage to win one of those fights, the game lets you continue and even gives you a special reward, though the game otherwise continues the same way. (There are other instances of this, but it's clear that you're not supposed to win, like the first boss fight where the boss eventually uses an attack that is not survivable at that point in the game, and it hits both your characters.)
* Final Fantasy 3's Cloud of Darkness. In the famicom version, you can cast Shell to reduce the damage you take to 1, but you have no way of doing damage, so at this point you are stuck, particularly since you have thousands of HP at this point. There's also the early Bahamut fight, who does very little damage and takes decent damage, but who refuses to die (too many HP and fully recovers every round), so it's easy to get stuck here and not realize you're supposed to run away. Both bosses were fixed in the DS version; CoD will hit your entire party for (displayed) 9999 damage in the fight you're not supposed to win.
* Final Fantasy 4 also has one boss fight where, if you forgot to pick up a certain item in town, will just do 9999 damage with normal attacks and where a party wipe is an actual game over. Only by getting that item first can you continue past that fight, and if you didn't get it before hand, you have to go back through one of the game's most annoying dungeons.

Oh the game is pretty terrible in many regards, but it has that Diablo atmosphere and esteatic which I find great and in this game it actually makes sense to choose a priest over a fighter or sneaky type.

Eh, given i always do that anyway,this one not so much. I mean, sure, it could be worse, but i was expecting better.

Since nobody mentioned it:

Life is Strange.

I adore the game, it made me laugh, it made me cry, but the end choice is simply shit. Those who've played it will know what I mean.

i liked the end

Of course. You like fish.

fishes are cool i have plenty

Ghost of Tsushima.

Despite overall being a good game, it forces you to the terror path. Even if you avoid it as much as possible and never choose to use it and always fight the honor path when you are given the choice, the plot forces you a few times and mandates going in that direction. I was quite disappointed they forced it. Sucker Punch's previous games have been good about at least having a binary "prosocial path" and "antagonistic path" (in Ghost, it's Honor or Terror). There were even elements of Ghost that seemed to indicate it initially was going to go that way too. It was clearly cut to make release, and the game is worse for it. There's one place where it almost matters around the end of the game, but, even that one has a forced resolution and is mandated because of the requisite terror story.

[Again, it's still a good game, as open world combat games with "base clears" and TACOs go.]

Reminds me of Etrian Odyssey 1, which is a good game except for the fact that it forces you to genocide the dungeon's Indigenous population.

Etrian Odyssey 2 is better in that regard, but I found the game balance to be worse there, favoring overly offensive set-ups and punishing the player for using stat boosting songs.

Edit: EO3 gives you a choice, and is better balanced than the earlier games, but suffers from the problem of boss fights being too long (as opposed to EO2's too short boss fights; EO1's are what I would consider the ideal length).