I've played a bit of both the Steam "official" release and one of the recent "experimental" releases (on another machine, so I don't know which one; sorry) and both have a serious UI issue because of buildings obscuring parts of the map: I can't see things my soldiers can, which means I can't have my soldiers shoot things that they can see. It's clearly intended to work -- Xenonauts renders buildings transparent when your soldiers are behind them -- but not when your cursor is over them. This makes it way harder than necessary to shoot aliens in the street "behind" (from the camera's POV) a building, especially near the edge of the map, where clicking on the alien-head icon doesn't (can't) actually center the screen on them. (It's frequently hard even when it does, because the screen is frequently a sea of absolute darkness.) It also makes it extremely difficult to order a soldier shoot at an alien in a building from outside of it. (This may be a difficult task to perform, but that doesn't mean it should be hard to order someone to try.)
I think this would be mostly resolved by having the "height bar" (lower-right of the screen) be a global control -- right now, kind of like the transparency, it only functions when a soldier is inside or right next to a building (or vehicle). This makes it almost useless as a way to get minimize how much of the battlefield is obscured by the camera angle; I'd like to be able to shoot the alien in the street from much further away than the base of the building its standing next to.
Another option, of course, would be to have the buildings become transparent based on where the cursor is, instead, but that may (I don't know) cause problems in terms of targetting the wall(s).
It may also help to render aliens that your soldiers can see (e.g., whose icon you can click on) fullbright (like the UFOs for that one bug), although I could also see that being deceptive.