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.

Observation and Deliver us the Moon

If you liked chants of shenaar, check out heaven's vault. I think it does what chants of shenaar does, but better, and it did it years before. It was a bit strange to me to see chants of shenaar get so much hype, but have heaven's vault stay slept on.

Breathedge - SciFi game where you are stranded in a small shuttle after your main ship exploded, you'll need to fly around in a space suit with limited air supply, gather stuff, examine objects to identify possible devices you can cobble together from random space trash, and eventually build and upgrade your equipment to the point that you can progress to another area, and so on.

Once you know how specific items are built, the solution is near identical, just some components might be drifting in another part of the screen.

I personally think the main series Danganronpa games alongside Despair Girls have enough of a play through the main story mode (don't know if there are any other modes for Despair Girls) and then you don't replay almost ever type of gameplay since they're visual novels, technically. (I don't consider them visual novels because I consider those to be just images/animations and a text box on screen with no control over a character).

The 3rd game even has a mode you unlock at the end that has replayability, though, so I don't know if that would disqualify it.

Also, another game I like with pretty much no replayability besides watching your favorite scenes play out would be the point and click adventure game Beyond the Edge of Owlsgarde. It's a game that, if you know what you're doing, can be completed in 2 hours. My first playthrough took a lot longer though, since I didn't know what I was doing. Also, it only has 2 endings and if you miss the good ending, you'll get a hint at the end of the bad ending which will guide you to the good ending.

I would say Stillness of the Wind definitely falls into this category. A beautiful game about life and loss.

the desolate hope. its a very unique robot themed game, but you only really need to play it once.

There is a game from the MS-DOS age of 1996 called Realms of the Haunting where you traverse large open areas for hours searching for items and interactables needed to progress.

You might clear it a second time just to make the experience seem like a linear cohesive string of events but I can't imagine you would want to clear it any more than that.

as much I love the genre, but most single player 3D action/adventure platformer games that are based around a story OR fully arcade-y.

both aspect looses their point if you 100% the game.

Like, I just finished New Super Lucky's Tale, and though it was an excellent 3d platformer, I don't think I'll start a new game.

but not only 3D games. Like Shovel Knight also falls into this category. Amazing and exciting game, but other than a harder difficulty (as New Game+), it doesn't really have too much of a replayability.