This is more of a generic topic of observations regarding most Zelda games, or heck, many RPGs in the first place.
1) Dungeons seem far more dynamic than they normally seem.
For one, why are they called temples? You've got your fire temple, your water temple, your forest temple... so if they're a temple, who prays in them? Where? Are there prayer books and a pulpit? Is there some dais where someone leads prayers? Is there some sacrificial pit where a lamp is sacrificed to appease the deities? Who built the temple and with what funds?
Who keeps a map in a chest on a high-up area? Who stored a compass in a hidden chest behind some vines? Why are so many doors locked? Who's scattering these keys in different areas of the dungeon rather than them being on a keyring by a maintenance fellow? Who cleans these temples? Who gets hazard pay because the temple is flooded or filled with lava? Where's the accountant? Where's the storage room?
2) Same dungeon, different dungeon.
Everyone has a fire temple, an air temple, a forest temple, etc. It's just what you do. But they're always different, but it's the same world. Has there EVER been a series where a temple or dungeon is the same between games, and you're visiting the same instance of the dungeon only with slight differences? I think the only occasion I can really remember is how in Deus Ex 1, the first area you visit, Liberty Island, is the last area you visit in the sequel, Invisible War. That gave me awesome shivers. But that's about it.
Why do they keep needing to rebuild them, anyway? Does the geography of the area shift around SO MUCH that they have to rebuild and rebuild these temples, and even in a different location? Sometimes the land mass doesn't become volcanic or get flooded. Why not make a building a historic monument? But seriously, who is getting paid to build these things?! Is it slavery? We all definitely take it for granted that the buildings simply exist.
3) There's treasure under those leaves!
Why is it that when we slash a bush, it practically explodes and drops a rupee or some weird heart thing? Why is it that when we slash a pot, it drops money? How clumsy are people that they're dropping single or 5 coins worth of money in them all the time? Maybe even arrows?! What's up with THAT? Who just walks around with arrows and is constantly dropping them into pots?!
4) Monster gates?! More like monster mysteries.
How the heck does a door slam shut when there's a monster that you have to kill. Who designed these massive complexes with some kind of trigger that detects one kind of life but not another kind of life. It's not like it's usually a force field generated by some dormant but still attentive deity, either. It's an actual gate that locks or drops down and only unlocks when you've killed the monster. Plus, the monster was already there in the first place, and the gate was open! It only closes when you yourself enter. It's like it knows that you're a hero and you're the only thing that can cleanse the threat. So, who's watching that function of the dungeon or temple? Is it the deity? Or is it the maintenance person? Maybe they're just shy and don't have a speaker system to communicate with you.
I think if I ever make a ZC quest, I'll have a maintenance guy chat with you as you're walking around the dungeon. I think that would be a fun idea. Don't you? Just general chatter, actually! "I'm so lonely. Want to talk about food? My favorite food is pizza. I make it right here in the dungeon." Then there's actually a real room you can walk into that has a few ovens and scattered ingredients. "Whoops, must've just missed you. I'm in my private washroom right now. It's real fancy in here. ... Don't come in though. I don't want you touching anything with your bloody hands."