I came to this thread with one idea, read what Shadsie had to say, and suddenly... boom. Idea idea idea idea idea
This is entirely possible, and I'd love to see this type of concept brought into real-time. If you pull certain themes form past temples that flopped--say, the Palace of Twilight, Jabu-Jabu, City in the Sky, and perhaps the Tower of Spirits, and some ideas form mini-dungeons such as the Gerudo Training Center(whatever it's called, that place with the ice arrows) or the harsh complexity of a Water temple, put the blender on high speed, and make an incredibly cruel dungeon you won't want to set foot in.
Perhaps you could draw on the Colossus in Shadsie's post, and know that the dungeon IS the boss form the start. Then get the shock of your life when the goliath dragonlike beast changes from armored beast to crypt and joins with the stone ruins of an ancient place--makes me think of the Gerudo Valley after OoT. So you enter the crypt under the assumption that you'll find it inside, without knowing the truth, and slowly but surely get hints that the creature has somehow BECOME the broken temple. You find strange, fleshy-pink walls everywhere, surrounded by deadly, bladed traps that get harder and harder as you circle through the spiraling corridors and reach a pulsing, writhing mass of evil aura--the monster's heart. It is here that the true boss battle begins--the darn thing takes flight with you still inside it, reordering the dungeon's puzzles and eradicating your precious shortcuts. You lose soemthing really important--a crucial item or something--and have to redo it without it, knowing that to fall through the temple means to hit the ground hard and ahve to redo that phase, and that to stay too long is to be digested.
Boom. Dungeon.
Yes, I want to see this happen.
Also? Holy [CENSORED] I
HAVE to play Shadow of the Colossus! I know how it ENDS and I've never played it!