I think there are a lot of things left for me to learn about tiles and auto tiling, but from what I've seen there are some features that I can envision that would be nice to see from YYG eventually that would further enhance what they've done for auto tiling.
For example, from what I've seen so far, there doesn't appear to be a way to work with two different sets of auto tiles in a way that allows them to blend together. For example, if I want a set of tiles for grass land, and a set of tiles for a dirt road, blending the two together so that they look natural is desirable, but I don't see how to do that yet with the built-in auto tiling. I'm not sure if this is just my inexperience with auto tiling, maybe there is a way to do it and I just haven't thought through the capabilities of what's already there.
I like the idea of an alt-set for auto tile, since it would help to break up the visual monotony and make for more interesting designs without adding a lot of extra work for the developer when laying out a tile map. What I can offer instead, for now, is to create an alt set of tiles, and apply them over the original auto tile layer, in a new layer. The alt tiles don't necessarily need to be a complete set of tiles, and do not necessarily need to be an auto tile set. But having a set of "decorative" tiles that add things like extra rocks, tufts of grass, cracks or texture, etc. that you can spot-place here and there, can go a long way.