Dungeons are supposed to be the central gameplay draw of Zelda. They’re where the player achieves the vast majority of their progression, both on a smaller scale with the items that they obtain and on a larger one with the milestone that the player crosses upon completion of the dungeon.
Because of this, dungeons need to be where the games challenge is at its highest point.
To answer the more specific points, a dungeon needs to be on the longer side. A good dungeon not only needs a central mechanical theme, but it needs to have enough time to develop that theme in a natural way. That doesn’t mean that a longer dungeon is always better. LttP’s Hyrule Castle and Ganon’s Tower are both prime examples of dungeons that are way too long without ever doing anything interesting with their length. As a general rule of thumb though, a dungeon should be something that the player should be spending a lot of time in.
I think complexity is a better metric for a dungeon than difficulty. Difficulty can also refer to combat, which has never really been the focal point of a dungeon. Dungeons should try to he as complex as possible, especially the later on in the game they are. A good dungeon should preferably stump me at least once the first time I play through it. If it doesn’t force me to stop and think than it’s a bad dungeon.
Most importantly, that complexity needs to revolve around a central mechanical theme. An idea that needs to start out at its most basic and evolve until it reaches a climax at the end of the dungeon. This is why BotW and TotK fundamentally fail at having good dungeons. Even if they have a central theme it’s almost never allowed to build off of what came before it. Each individual puzzle in these games needs to be designed as if it’s the first puzzle the player experiences. This also applies to the games structure on a more macro scale. The game needs to be linear on some level. This is non-negotiable.
Atmosphere is less important, but it still can make the difference between a “good” dungeon and an “amazing” dungeon. I think the most important thing about the atmosphere is that the dungeon needs to feel like it was built to serve a specific purpose, which I think very few dungeons outside of the ones in SS do an adequate job of.