DanganRonpa and Catherine are two games that have already been mentioned a ton in this thread, so I won't go into detail there.
The Atelier franchise is one of my favourite franchises, full stop. They're incredibly cozy games, the alchemy gameplay is really involved and fun to minmax, and I like hanging out with the characters and doing all their questlines, even if the writing is occasionally really trope-y. But I find it hard to reconcile how family-friendly the games are with the occasional (and sometimes flagrant) fanservice. This is true of a lot of Japanese games, but because Atelier is otherwise a pretty wholesome franchise, it really sticks out there.
I also love the Yakuza games, and I think as time has passed they've gotten a lot better about this, but I do find that they rely too much on the male gaze and traditionally male perspectives on women. The games often have difficulty finding ways to include women as significant characters outside of people to be rescued or characters who offer emotional support. Yakuza 5 is one of my favourite games in the series partially because it gives Haruka some actual agency for once, at least in her segment. There's also this uncomfortable contrast between female characters we're expected to identify and sympathize with, like the main hostesses in the Cabaret Club minigames or the girlfriends in Judgment, versus female characters that are really only there for eye candy like the gravure videos in Yakuza 0 or the catfight game in Yakuza 6/0.