I'm coming back with a few more questions here... :p
First, obviously, I wonder if you have any intentions to work on a VX version. I don't think it should be too much of an adjustment (well, depending on how you translated the tilemap data...), so yeah...
Second, I've been wondering if you plan on creating a complete 3D engine, or if you'd try to support character sprites as well. That's a topic I'd instantly work on as soon as I'd be seeing some code from ya, so work on it yourself if you don't want me to put my hands on it ^^ (either way, only if you make a VX version :p )
In relation to that, I wonder how your camera's set up. Judging from the demo game, you have a position (x, y, z), along with a direction (an x,y,z target?). In that case, I'd figure you'd set that target to player coordinates as soon as there'd be an actual player character to focus the camera on, huh...
The other way I could imagine you doing it would be using angles (like, rotate camera 40° on x, 35° on y and 12° on z). Thinking a bit ahead, this might be easier to work with for non-scripters trying to adjust their camera later on, but harder to work with in scripts... (especially a sprite-based one)...
Also, I wonder what your plans regarding modelled environments are. I'm talking about cliffs and all that, but while complete 3D maps would be fancy, I think it'd be cool to instead have placeholder tiles for models.
Meaning, you place tile #12 of your tileset somewhere. That tile can store images of knights, cars or porn as far as we're concerned, because it'll be replaced via script with a 3D model that's perfectly cubic in it's outlines. This could be some cliff tiles, for example - modelled beforehand, like this:
I think you can see where I'm going with this. And yeah, that's all the poly you need for this size really, since anything else can be done with the texture (hint on the people posting models in here that, while showing skill, are too high-poly for their purpose).
While modeling this, I've been wondering if you'd include displacement mapping, since that'd sure be something neat to have :p
EDIT: I forgot to ask - for those 3D tile-mapped cubes you have, are you going to include any way you can assign textures to top and sides that are different from each other?
Also, I'm not worried about if, but WHEN I'll be able to take a look at the coding