I found the previous page's discussion rather nihilistic and silly. Glad it's over.
Anywho, I've been messing with irregular (non-cube) tile shapes, and came up with the following:
Going to get all the Natural Stone Tile types down using a similar geometry, so ore veins and gem deposits can be layered over base stone tiles. (There's a simple Moss texture here showing the same principle behind this; the tiles are designed to have divisions in certain places, so that one Moss Overlay can be put over natural sandstone pillars or Stone Block Walls, and it will look as though it is growing in cracks or along contours.)
The tiles have been redesigned so that a black hollow area is on the top of all Wall tiles, so that when viewing in the underground layers, you can quickly tell that the you're not at the topmost layer. Any walls without floors on top would display with the top part black implying a cutaway, and you can also use the half-tall cutaway blocks to display interiors in single-layer view, or in the case that simple foreground wall cutaway logic is implemented... rather than those Cyan thatched block things that are currently being used.
Also, you might notice the tiles with and without borders. The bordered versions are for displaying on edges so you can tell same-colored walls from floors, while the unbordered versions are for displaying multiple contiguous walls. You can cut and paste certain parts the bordered-tile graphic and overlay them on the non-outlined tiles when there is open space adjacent to them, to create dynamic borders. I suppose you could instead code the engine to learn to recognize the edges of 2D graphics, and draw a shaded border along it as needed that would work as well, but that sounds like it could be a pain to code.