Hm, I could see having a two-layer level instead of a three.
I've seen it on a old old game called "bugs" or "bugworld": the level was 64x64 I think, and tile-based, but two layered. The lower layer was the ground tiles.. you could walk over these, no matter what tiles they were (besides lava and water, which you'd 'swim' in.. the game didn't have swimming), and the second layer was for walls and objects such as health and ammo. What was really neat about it was that not all tiles were completely opaque, such as the rune tiles. These blocked player movement and were small glowing symbol-like images with the rest of the tile transparent, so you could put them on a wall tile to make it look like a wall with a rune on it. Also, since there are two layers, you can put wall tiles on the bottom to make it so you can walk over them, thus creating hidden paths for the player to walk over.
I could see adding a third layer, too, that would be drawn over the player, but that isn't really necessary, though it would be fun
Leveling on that game was fun

you had 128 tiles total, but with two layers, you had a ton of choices. 2^14th to be exact
I know this is rather different from your idea of multi-level where each layer is a separate level, but I think it would rather come in handy, and wouldn't be much of a change from the current system, and would be a hit with the levelers out there.