I agree, unhappy endings are a fine change of pace, when they're done well and fit the mood of the game. Some of my favorite RPG endings have been those of Shadow Hearts 2 and Rakuen, and I quite respected the endings of Severed and Eternal Senia 1. Unfortunately, I don't feel that the ending of Witch Hunt does either.
First: Regardless of intention, Witch Hunt isn't a cynical, twisted tale until this very ending - the setting's elements of horror and the evils wrought by the Devil Witch aren't enough to make it so on their own. Cybel herself is relentlessly driven in an outgoing, good-natured, and well-intentioned way, reigning her party members in to focus on the task at hand when necessary, insisting that they do the right thing for those they pass by even if it inconveniences her party, and always ready to argue against a bias that witches are all bad. No part of her is cynical or twisted, nor does any part of the game's events, cast, or theme make any real effort to make her so. And since this game centers around her personal quest, and since her attitude and interactions are what define the party's dynamic,* it does not come off as cynical or twisted as a story at all.
* Not that said dynamic would be cynical or twisted even without Cybel holding it the cast together. Xendra's a prideful professional, Xena strikes an appealing balance between a fledgling warrior adventurer and Cybel's supportive bestie, Viktor's a cowardly lion type, Marvel's a focused professional who takes a slight distance of distaste from the rest, Double 0's a damn chicken, Sandy's mostly just there, and Lone focuses mostly on just getting the job done rather than what he's lost. There's a lot of bickering and they aren't all skipping around with their hands clasped in friendship, but no part of the dynamic overall suggests anything cynical or twisted beyond
maybe Diddy, who's more just puzzling than anything. With the Bear's abusive negativity and Jezebel being a jerk all around, I'd say the cast of Millennium's being forced indirectly by an oppressive government system to work together with people they could genuinely dislike, sometimes for reasons that aren't inspiring and nice (since Marine has to practically force some of them to be there) would actually have made a more compelling bid for cynical and twisted.
Also, the very foundation of this game's story works against the idea of it being cynical and twisted. Cybel's boyfriend got transformed into a chicken - a chicken with an amusingly exaggerated profile picture, to boot - and she's embarking on an 80s-NES-styled quest to fix him. Even if everything else about the game's events and characters and feel lined up toward a cynical and twisted mindset, it would be difficult to square away with the spiritual foundation of Witch Hunt.
Second and Far More Important: I'm not disappointed because it's not a happy ending, I'm disappointed because it's careless and just abruptly drops. There's a world of difference between an ending that doesn't intend to resolve everything and an ending that doesn't try to resolve
anything, and there's a world of difference between an ending that's not happy and an ending that's simply incomplete. The reveal that
the chickens got switched is made,
and things just stop there. That's it. There's no emotional payoff of any kind, positive OR negative, there's nothing to take from it, there's not even enough time devoted to this ending for it to feel cynical or twisted. It's like a conversation where the battery in someone's phone dies mid-sentence. The true weight of what's happened doesn't have time to sink in for Cybel. We don't get to see any of the lasting results of what this will do for her relationship with her parents, nor how it will relate to any of the political circumstances surrounding witches and Wes's family which the game dropped on us just a minute before (which, by the way, is also not a good move; the ending isn't the place to drop the majority of the game's social lore). We don't get to see how the rest of the party reacts to this news and interacts with Cybel over it - we didn't even really get to see them react to the revelation of who the Devil Witch is! 7/9ths of the major cast members of Witch Hunt end this game
waiting in a hallway. There's not resolving everything, and there's not resolving
anything, and it's the latter that Witch Hunt does.
It doesn't feel like you wanted to make a twisted, cynical ending without full resolution, it feels like you just didn't want to make an ending, period. Witch Hunt didn't end, it just stopped.
There are other, better ways this could have been done. Off the top of my head:
Rather than just fade to black with a teasing message that leaves the player wondering whether they'd done something wrong somewhere down the line, continue to another scene, with Cybel and company returning to the Monastery. Have them go back and legitimately not be able to find the real Wes, and show the emotional fallout of that. Did something happen to him after they accidentally left him behind? There aren't enough monks to watch over this place any more and there's monsters all over the place. Did he just wander off? They'll never find him. Did the switch even occur here? It's the most likely place, but it's possible they could have accidentally grabbed the wrong chicken anywhere. It could be a dawning horror on them that they'll never find him, if there's even anything left of him to find. This scene would give you time to show the true weight of horror as it sinks in that she's lost him for good. It would give you a chance to give the rest of the party some time to react to this, to interact with Cybel over this matter, to sort out their own final feelings on the quest and the twist and the tragedy. When all is said and done, Cybel could rush outside and start frantically calling for Double 0, ignoring her friends, ignoring her mother, searching in desperation that we suspect is fruitless. THEN fade to black, maybe have a tasteful bit of narration about her having accomplished something good and important in stopping the Devil Witch, but at the cost of perhaps never knowing the fate of her boyfriend and the guilt of such a simple mistake costing her so much. There you go: still cynical and twisted, definitely not a happy ending, and the most important thing to the whole game (Wes's fate) is left unresolved, as well as how this will affect the kingdom and Cybel's future as a ruler and/or as a witch...but it still has the payoff of emotional fallout for Cybel, it still has some degree of resolution by having the rest of the party able to say their piece and perhaps indicate what they'll do now instead of locking them in a waiting room and forgetting about them.
Would I have liked this? Goodness no. Because it's still highly contradictory to what Witch Hunt is as a game, regardless of author's intentions. But it at least would have felt like an
ending I disagreed with. And this is just an example of a possibility; there were many different ways to play this setup in a way that would provide a definite conclusion, unhappy or not, fully resolved or with an appropriate number of matters left ambiguous, to your game. As it stands, the last moments of Witch Hunt don't feel like you wanted to do an unhappy ending, they just feel like you wanted to wash your hands of the game and move on to the next as soon as you could.