I've messed around with dungeon methods quite a lot, Captive is my all time favorite game and plan to make an awesome dungeon crawler inspired by it.
3D all the way, seriously these games were only 2D because 3D wasn't available. The map itself would be 2D, just like PSY pointed out, then these 2D tiles become 3D objects. Because frame rate isn't a massive concern, you could render to an image for example and add depth of field, refraction, reflection etc etc, make it really shine. There are some real nice shaders available for AppGameKit now, there's no reason why your game shouldn't look awesome in AGK.
Really there are a lot of benefits in making this sort of game, like path finding for example - it can be a flood fill based system, very easy to impliment compared to A*. Occlusion would be quite straightforward too. I'm sure there is a reasonably good market for these games too, people like slower paced RPG's, a lot of people just don't like games like Skyrim, and prefer slower, methodical RPG's. I'm always looking for dungeon crawlers on the app stores.
The code is dark and full of errors