I have also been poking at a shopkeeping game on Kongregate (more grindy than I'm happy with but there are some time-and-motion optimizations!), and thinking of either getting back into Dwarf Fortress (also big on time-and-motion) or finally learning how Towns works.
Not that I have time. Especially this month. However!
What I'd really like to see is a mashup of the two genres. Instead of playing the dwarves tunneling into the earth below, play the nearby human town they trade with. When the dwarves discover a good seam of iron, you can trade it with visiting caravans, or build a forge to sell the iron back to the dwarves as pickaxes and armor. But if you don't take the latter route, the dwarves may decide to invest in their own ironworks, reducing the supply of raw materials--- but potentially opening the door to higher-value goods. I'm imagining both tactical decisions on what facilities to build and what goods to stock--- but also a strategic game about developing trade and competitive advantage, exploring a tree of different decision points.
Most shopkeeper-type games tend to be more about collecting everything rather than specializing, alas. And most trading games are mostly about established patterns rather than industrial development. I'd like something a little closer to SimCity or Civ, with multiple paths to success.