Example; the Legend of Zelda: BotW and TotK weapon degradation system. At first I was annoyed at it, but once I stopped caring about my “favorite weapon” I really started to enjoy the system. I think it lends really well to the sandbox nature of the game and it itches that resourcefulness nature inside me.
It has dungeons: The four divine beasts.
IMO It put a lot of the “Use a particular tool for this” puzzles into the shrines to scratch the puzzle solvers itch, (along with some of the Korok seeds.) but even those still gave leeway to not having to use those tools at all.