Nice thread, many of these suggestions are great.
I specially like the 3D terrain (bubbled of water and air, underground rivers with banks, stone formations in 3D etc), the antmen suggestion and burrowing.
about airflow. wouldn't the easiest way to do it be to dig a shaft straight down to make a low placed tile "outside", and either count 8 squares from there, or place a fan (must be inside, bordering on "outside" and be mechanised), which increases the number to 16.
so 1 shaft in the middle of the fort ventilates a circle around it with a diameter of 32. A mining shaft would then go rather straight down as this is the easiest to set up (just add fans on every level and increase power) instead of being across the entire map, mining out every single tile in the mountain. This would surely also help in making engineers more important in any mining operations.
It might be buggy if this doesn't take built walls and enclosures into account but I could live with that. One would also have to assign all features as automatically "vented" so avoid creatures in them suffocating to death.
and my own suggestion:
I would like soil tiles to randomly "caving/filling up". Occasionally a tile dug out of soil would "cave in" and the tile become soil again. this does not affect tiles above as in a normal cave in. If creatures burrow in soil, golbins dig through it it would "clean" the tunnels after a while, and rooms in soil would have to be redug every one and then or walled and floored properly.