My favorite h-game stories are ones that emphasise the vulnerability of the MC. Obviously this must be reflected in gameplay too. I don't so much enjoy playing as ultra-powerful magical girls unless they have weaknesses in equal measure. Take for example Wanderer Girl Rei
https://ulmf.org/threads/rei-wanderer-girl-rei-combat-rape.10893/ - As far as I could understand, the protagonist happens to be extremely skilled in swordsmanship but is otherwise completely ordinary. Gameplay revolves around preventing her from being disarmed through stamina management. Or Taima Shaman Miko/Exorcism Shrine Maiden. Both its characters are (or become) crazy powerful, but the enemies' H-attacks drain their magical power and many of them can bind her to prevent her using physical attacks, and making her even more susceptible to H-attacks.
As for the plots themselves, in my opinion John Carmack was right when he said "Story in a game is like a story in a porn movie. It's expected to be there, but it's not that important." when you apply it to H-games. Anything more than creating the context of the gameplay, giving the character their backstory and motivation, and those of her adversaries is superfluous. It can be nice and it can create greater context, but often it runs the risk of detracting from its eroticism if the subject matter is too heavy (Phantom Gate, Reclaim Reality, TSM). Unless you're a snuff or guro fan I don't think hentai and references to death, injury or malady really mix. Or to put it more succinctly, experiencing an H-game's story shouldn't be upsetting.