They don't exactly fit with your theme of short mystery and puzzle games, but based on your initial question most JRPGs and most story-focused games came to mind. Let's go over a few of them I'd recommend to everyone interested in those games:

• Persona 5 Royal: It's about a 100h and very story-heavy. There are some twists and turns which keep you engaged and you build relationships with a wide cast of characters. Besides the story and actual combat, there's a ton of side activities, all of which you only do a few times. It's probably my favorite game I'll never replay, because all these things are an absolute slog to play again. The same goes for Persona 4 and maybe 3, haven't played that one.

• every Etrian Odyssey: They are old-school dungeon crawlers originally released on the 3/DS and got remakes on steam and the Switch. You draw your own maps of every layer the dungeon has, which is a large puzzle in itself. However, once you know the dungeon, there is literally no point in exploring it again. You know every trap, every worthwhile detour and of course the path to take.

• Like a dragon 7/8: They combine an open world with lots of mini-games, funny and/or touching side stories and an epic overarching main story to follow. There are tons of interactions with your companions, all of them interesting. It's just, similarly to Persona 5, all these mini-games and interactions only carry themselves for the short burst you get them in and while they are fresh. Replaying them? It's an absolute slog. You know every punchline, you have optimized most mini-games and probably remember most of the great backstories each character has - you'd be skipping most of the content and the non-optional combat system isn't fun enough to carry itself on its own.