Well, now here's an idea. There's currently only one layer of dungeons, right, with just empty space above and below it?
Well, how about putting in two or more layers of dungeon, and connecting them with intradimensional portals? That would not only make the maze more complex, but also allow non-Euclidean geometry like 720* loops. If XCompWiz ever updates Looking Glass API to 1.8, you could even make the portals seamless (and since it's within the same dimension and even the same chunk, there would be no load time).