Surface and above Z-levels are probably the biggest pain.
I've often thought about just getting rid of these views and showing only Z levels. It's been a really long time since I've played Dwarf Fortress, but how does it handle this stuff? Does it provide surface / top down views, or does vanilla DF only show one Z level at a time? A part of me thinks that by adding these convenience views, I've just made things more complicated for users.
My memory might be wrong... but its cause you have trees blocking the view between the leaves and the ground. This sort of thing probably needs a better visual indicator that you ain't actually looking at the ground.
Also an easy to see indicator that the ground isn't flat.
I've tried pretty hard with this, but some of the rendering options might be buried in a place where users don't look. If you open the advanced view options dialog (clicking on the eye-button in the toolbar), there's an option called "Enable Elevation Shading". It renders lower tiles darker, and higher ones lighter, to give a quick feel for the terrain's slope:
You can also check the "Show Elevation" option, which will render a number on each tile, showing its Z level.
Still, even with all these attempts at making everything intuitive, the result just isn't smooth enough. I don't know if there is a great way to render a 3D world from the top down, as Outer Colony is currently trying to do.
With that said, though, I'm really attached to the 3D, volumetric nature of our world model, and I don't want to abandon it. I see some of you guys like it quite a bit, too. The possibilities it opens up are just too great to walk away from, so we're going to stick with 3D, but we're going to change all the graphics to use isometric pixel art, rendering the world in 3D from a fixed angle, like Stonesense does. It's going to be a ton of work, but I think the end result is going to look great and be much easier to play.
Wish us luck!!
Oh, and Tchey, I promised you a tour of Voyager Games corporate headquarters! Here it is, man:
This is where Outer Colony gets made! It's not much to look at, but really, what more does a software developer need? A folding table, a comfy chair, a computer, and a quiet room. That's all anybody really needs to do this sort of work, I think.