Actually, this might be really interesting, essentially turn the world map into a full 3-d map itself rather than just the 2-d one it is now, so you could see the heights of places directly, and scroll up and down between layers. Have the world map with a large number of layers/world map layer, and then regional and local views would be more finely detailed. Local ones might be only a few layers/map layer or something, make it easier to see the general height of an area.
And for example, instead of a tile just showing that it had an underground pond in it, you could look and see where it was vertically. Or see that a tile had an underground lake 2 world map layers down, an underground river running through the 3rd layer down through the third tile(and where all it started and went vertically in it's process), and some adamantium 4 layers down in the same square. Set up world gen to be really 3 dimensional in how it places things.
And then a really useful part, you could have it set up so you could designate vertically as well, make your fortress 3x3x4 to get to that adamantium down there, or such.
Although that might end up with some tricky to handle forts that would require some extra code. Next to an ocean where the region doesn't reach the bottom, on the side of a mountain, where it doesn't reach all the way down to the ground. Those wouldn't be too hard I suppose, you could just create an air/ocean tile for the bottom of the map, that would act like a chasm/lava flow, etc. Or if you start out in a cavern where your region doesn't reach the surface.