Fluidity, if the dungeon doesn't "flow" right, by this i mean look at stone tower, excellent dungeon but quite often you have to puzzle your way around to find the right way forward, for the dungeon to flow right you have to feel like you are always moving forward such as Ancient Cistern you were constantly moving through the dungeon and it never felt forced, it was an organic progress.
Decor, if the dungeon looks bland as hell, such as Fire Temple, then theres not really any reason to look around you just rush through things.
Attention to detail/puzzles : in the early zelda games i recall a dungeon that used the bomb arrows, something at the time no one really realised, the bomb arrows weren't a really known thing back then(i think it was LA in fact) i think dungeons should maybe use little known techniques or abilities not as a central mechanic but as a way to give little shortcuts or hidden areas for rupees, MQ did this with it's fire temple and OOT on the whole with it's special fairies, in terms of puzzles it can't be something that'd force you to google it, the answer should be self evident such as the OOT Poe Sisters or MM's Great Bay Temple.
Detail: Always ALWAYS details no point in having bland monsters or chests in yer dungeon what kinda hero is gonna show up for a bland adventure? give us that gilt banding around the walls, discoloured bricks and funky room designs.
Bosses: if the boss is a boring boss then temple is by definition boring, look at some of TPs bosses Fyrus was a boring ass boss as it quite literally capitalized on the ole eye formula, Diababa was a riff on King Dodongo and Morpheel was just a Morpha remix. TP on the whole Abused the Eye formula, in what world would a freaking dragon have an eye on it's back? Especially an Armored Dragon, way to blind yourself.