I'd like to see something like the Skull Woods dungeon from A Link to the Past, where the dungeon is effectively integrated into the overworld. Skull Woods did it to a small degree with having to go in and out of the dungeon, creating a maze-like environment, and having to maneuver around the overworld obstacles. I'd like to see them take that same concept a step forward for a 3D Zelda, and really make the dungeon and overworld an "interlocking" and codependent environment.
One possible scenario/theme could be an overrun town that has been taken over by enemies, and the "dungeon" essentially becomes the town itself and/or an underground component created by the enemy which interacts with the buildings and townfolk above. The dungeon would require transport up to the buildings within the town through ladders/elevators (whatever the mechanism may be) that open up from trapdoors into different areas. You interact with the townfolk while you move through the dungeon (they may provide you hints, allow you to purchase items, etc.), and some of the buildings may be "open" to allow you out into the main overworld while other buildings may be locked. You have to figure out when and where to move up into the town in order to get to different areas of the underground component of the dungeon.
The key to this idea is that you could actually leave the dungeon/town area and move into the rest of the overworld whenever you found yourself in the town,even if you had not completed the dungeon yet and come back to it when you wish. You can obviously leave dungeons when you wish in other Zelda games, but sometimes the game does not progress until the dungeon is completed and the fact that this type of dungeon wouldn't be constrained entirely by walls would make it feel much more integrated with the overworld and may not even feel like a classical dungeon. I think this would really promote and support the idea of a less linear overworld and story flow that many Zelda fans are now asking for in a 3D Zelda game.