Wow that was a fascinating experiment! I liked how the music seemed to be linked to gameplay. I think your implementation of 2D ended up a bit confusing due to the ceilings coming in the way of play vision. Also the enemies should not be able to shoot you when you're not able to see them from the top down view is an easy fix.
Other than that, this is a well thought out prototype that really bended my brain a little, well done!