What if I stuck to an Isometric design?
It still looks a bit rough, but I actually like it better than the original map design. Mostly because it scales well with the player and enemies since they use 8 directional animations, so they already have isometric views when they go diagonal.
The original layout looked very bland, and it was very hard to decorate, but with this Isometric view, not only does it help show off the 3D element the original map was attempting to give, but it also helps give a better atmosphere with the 3D elements. I was struggling to find ways to make the original map at least visibly pleasing.
I also rearranged the players movements so when you go diagonal, it goes up at a slope of 2, so you walk parallel to the walls. Plus, I had to add a ton of extra code and bundles that changes the display order so the walls, player torso, legs, arms, and the crystal objects all display correctly. I wanted to get some feedback on this design before I make any rash decisions.