Well this is an interesting solution to a problem that has already been solved.
Problem: In adventure mode, if you want to explore a large dungeon you have to make your own in dwarf mode. This means that you know all the twists and turns of your fortress, and beyond finding a few goblins hanging out in the cellers, there is little surprise.
Solution: Well first and formost, people make large and fun forts, then trade them over the intertubes. It means some nce and unique works for you to explore and figure out. Secondly, we have the caverns. While these can be open and easy to move around in, they are hell to navigate... Once you go in, chances are you do not come out, making for great laberenths to test your survival, especialy in some mods that include more viciouse beasts. The problem is that caverns are rather unrewarding to explore. This can be fixed by modders, once again, by giving creatures unique drops, but it would be nice for toady to make the caverns a little more interesting, a great start being allowing us to give creatures weapons, rather then just entitys, but what ever.
So we do sort of already have natural dungeons, however, I think this suggestion still carrys merit. As Capntastic bought into light, reason is a nice thing, but not hard to apply. Even as hardcoded site tags for underground civs, the abilty for antmen to build underground citys and such would be a very nice touch.
So in the end, supported! I trust Toady to do amazing works if he picks this up, and it would add to the game a lot.