My big beef with WW's dungeons (lack of them aside), was the fact that they all felt really big and really empty. Like room, key, room, key, room, key, a hidden alcove for one of those hidden statues, room, key, boss. And ascetically speaking, I only recall Dragon Roost Island and the Tower of the Gods as having interesting moments to them (maybe Ganon's Tower if you count the road between it and Hyrule Castle). Whereas I remember the Stone Tower from MM because you literally turned the dungeon on its head, or SS's Ancient Cistern because of the whole life & death/Buddhist theme to it.
Also Ganon's Tower counting as a dungeon was almost as lame as Skyward Sword's final dungeon.
Eugh, I hated Skyward Sword's last "dungeon". I can't tell what I like less; the shorter final dungeon (surprisingly that's often), or a copy/paste one with an obnoxious maze design that solidified how often you have to re-tread old areas in that game.
I thought Twilight Princess did their final dungeon well; you barely see much of Hyrule Castle in many of the games so it was cool to make it a proper battle ground that was something between being both eerie and familiar.
I wouldn't mind Hyrule Castle as a "safe" place for once too... It's always been under some shitty influence and you can't seem to tread it without some asshole trying to kill you. The town's are fine, but shit turns bad as soon as you hit up the castle for whatever reason.
I actually really think you hit spot-on with the comment that WW's dungeons are often "big rooms". From what I remember, they were kinda like that... Again though, that sort of reinforces how the exploration was one of the bigger selling points.
And as much as I hated Skyward Sword, Ancient Cistern is probably in my Top 5 Zelda Dungeons. The execution, motifs, the cleverly worked-in Buddhist story (in Hyrule no less), and the badass boss fight (beating Koloktos just...felt...GOOD) were just a fine combination of well thought-out elements.
It becomes interesting to point out there definitely is a tier in what "good" and "bad" dungeons are. I definitely think the series needs to shoot at Fire-based temples in a new way... The Goron Mines were nice and different but took a while to navigate.