I've tinkered with the editor on this for a little bit, using "Super Mario Bros. 3", "Kirby's Adventure", "Batman", and "The Legend of Zelda". There were a few things that I've noticed with these games.
SMB3 is kind of difficult to edit well once you hit World 1-2, where you have the various slopes. I was hoping that the Cube or Full Cube settings would let me place the same front graphic on the top of the shape, but it didn't work. I ended up having to use "Font", which made the tops of the slopes completely black. A new shape option that would be identical to Font, but uses more than just the edges of the graphic to color the sides would be nice.
Kirby's Adventure and Batman ended up giving me a headache when I tried messing with them. I ended up having to download a pre-made set to give me a decent starting point. Would it be possible to have a "Blank Slate" option for situations like these, that renders everything as a flat surface that we can then start pulling and stretching to make our 3D versions? Also, being able to choose which color is transparent or if none of them should be would be nice. As it is now, Batman (which uses heavy emphasis on black to give the illusion of lighting and additional color) ends up with all transparent buildings where you can see through the bricks.
Legend of Zelda has a couple problems of its own. The majority of them have to with the way the shapes work currently. You either pull in a full square shape, or not at all. Mountains are near impossible to get to look good, since you can't pull out the shape of the mountain. The ability to pick a color and ignore it when you stretch a shape would help. Also, a wedge shape would be nice for top-down games like this, for characters like Link. Dungeon walls can be fudged to look relatively well using the Cylinder settings, but Link's kind of a special case.
As a more general request, can we have the option to have increment buttons for each number in the editor that adjust it by one, and let us see the result immediately rather than manually clicking "Adjust". It would be nice for detail work, seeing results much more quickly, and I personally tend to forget to hit "Adjust" to activate my changes, resulting in having to re-edit the same object multiple times.
Finally, I would like to make a bit of an ambitious feature request. Let's say that we extracted the graphics from our ROM using something like Tile Layer Pro. If we were to save the graphics in the same compression as the source game, so the emulator would be able to read them and match the data appropriately, could we possibly have the ability to create pixel-based height-maps for tiles? I'd imagine making a black/white version of the tiles in the exact same format as the original game, using four shades of grey. The emulator would start by matching up shapes with the contents of the ROM to figure out what corresponds to what. Then, it would check the color of the pixels and pull out each color a set amount based on the shade. We could do something like this to get a much more elaborate 3D effect. For instance, the curtains in Castlevania's first level would be able to be a separate object rather than having to pull out bits of the grey background as well, and we could get more detail in the shape. (Bad example, since the "ignore color" request would functionally do the same thing, but you get the idea.)
--- TL;DR ---
We need a new shape that works like Font, but uses the whole graphic for the sides rather than the edge color.
We need to be able to set up a perfectly flat canvas for a starting state to work with.
We need to be able to pick transparency for objects.
We need to be able to pick "ignore colors" for objects.
We need a simple wedge option for top-down characters.
Can we have "increment" buttons for each numbered value in the editor, with instant results instead of manually hitting "Adjust"?
*Pipe Dream Request* Can we create height-maps for individual tiles in a game, if we were willing to keep them in the same compression format as the source ROM using an external program?