I feel like I'm not spending a good deal of time inside most dungeons; even some of the larger or more difficult places like Hlormaren or Ald Redaynia feel kind of short. The largest dungeons I have explored are the main quest dungeons, like Kogoruhn and especially Arkngthand; are there any others? I'm craving some deep dungeon crawling.

yeah, the main quest dungeons are the main large ones. Morrowind had mostly small dungeons.

This might have been because in the previous game, the dungeons were all insanely long, almost masochistically hard in some cases, and the maps made no sense.

Most of the really big ones are part of the main quest, so you've likely seen most of them.

Some large ones:
Bal Fell
Falasmaryon

Arkngthand (you get the Dwemer Puzzle box here near the entrance, but the place is big if you explore it all)

Norenen-Dur (Tribunal MQ, although some of it is optional)

But really, you need mods to get lots of deep exploration into dungeons.

When I started playing Morrowind, I posted a thread asking the exact same question. Unfortunately, those few dungeons are pretty much the biggest you'll get.

Dunno if you'd count it as a single dungeon, but Mournhold's sewers are pretty damn extensive.