I see that we have very similar ideas on how to improve settlement gameplay. Just recently, Nachtfalter and I discussed some thoughts about that and wrote everything down in a blog article on clonkspot, which you might find interesting. (Note that it's currently only available in German, so some people from this forum will have to wait until we found the time to translate it.) The bottom line of the article is: Mining had almost no focus in the Clonk series so far. While it existed, it was just a minor distraction/annoyance from the other things you did. We think it's worth considering how to make mining an interesting and challenging task on its own.

> ceilings of lose materials like earth could come down and needed to be supported with beams. and we introduced groundwater: tunnels below the water level sources of dripping groundwater were created slowly filling all deep tunnels with water

I especially like these two "environmental hazards". Stuff like that could make mining more interesting and still feel natural.