What i would like to see as a improvement to the underground.
Is making it so that picks can be worn down and made not use able after a lot of use.
And that each different type of ore you mine, requires you to have enough skill and proper picks to extract it.
Roots would be a great improvement. Also not just one tile below the tree containing roots. Roots would spread out all over the place. This would make digging through the top soil much harder, since a axe would be needed to remove roots. New job for the carpenter
Also maybe dug out tiles which still have roots in place next to them. You can make it so that you can "Smooth / Engrave" the roots also.
Wouldn't also hurt to improve trees and make them grow bigger as time goes on in which they do not get chopped down. Also expanding the roots.
Giant Ants + Giant Ant complexes.
Line of Sight, If a dwarf cant see it, then you cant. Mainly this would be important so that you can dig out a ore vein, then wall it up, and not have too look at the Mined out Vein. Or maybe just a way to hide those tiles.
Maybe if there was a castle in a location which turned to ruins, spawn a dungeon underneath the location of the castle. The castle wouldn't be there, but there would be a dungeon left behind.