I guess I can try the gradated skies out. It would involve some extra depth calculations, but that shouldn't be so bad. There's also the issue of subterranean "skies". Right now it just uses '#' instead of the sky character. There are fewer options here, because if it's fading to gray or something, it can be confused with a wall.
Handling chained animals falling is Bloat255. Right now I think they just break free, or worse.
Yeah, you can dive and ascend in water in any of the 26 directions using shift/ctrl + direction.
There is no steam pressure. It's nontrivial to model that, though it could be done, especially if the steam never occupies a lot of map squares (in which case it can use the flow objects rather than a square-by-square property).
When I was talking about flying over something to drop something on it, I was talking about adventure mode. If you chasm an object over a creature, it should turn into a projectile over that creature. You don't have as much control over which items are dumped in which places though.
Siege engines don't really think about 3D now. All the 3D projectile stuff is on to-do, and I probably won't get to it this time around. On the other hand, armies are the next thing up after this, and that should include better sieges and so on.
Beasts kept in pits won't starve to death because nothing needs to eat except your dwarves. Changing this is difficult, because each class of creature (wilderness animals, invaders, pets, etc.) has different problems that come up if you force them to eat/drink.
You can rewall with anything you can currently use to make a bridge. So you can do use glass blocks if you want. Or you can place a window.
For the building menu, it's not the average distance, but the distance to the one it would select if you press the button -- that distance is updated each time you press it for multi-item buildings, so you can switch materials if you always want the closest.
The elevation number on the bottom is absolute elevation (100 is sea level, 150 is where mountains start). I wasn't looking during the movie, but if it gets up to 195, that would explain why that map has such steep cliffs (because the wilderness border is <150). The number on the top is levels above/below ground relative to current view. I used to use striped bars, but that was before there were wilderness altitude levels (that is, there was just a +/-15 levels, but the world was level).
Yeah, changing the name of pond to pit/pond is on to-do. It's sort of an animal pen, but always involves dumping. They won't bring an animal in to a walled off area and just drop it off at the same z level, so the dream of the corral/pen is still off in the future.
If you have reclaimed a fortress, you'll have become familiar with reclaim item/buildings -- it starts all of your old equipment/buildings as forbidden, then you say which ones you want to use. Unclaimed stuff is invisible to your dwarves. Now this has been extended to first-time forts -- you can forbid any item to make it invisible to your dwarves, and reclaim it at a later time.
Yeah, rock salt is a new mineral, though you can't do any saltish things with it yet.
You can dig a hole in the ground using the "channel" designation. With channels, you select a floor, and a dwarf, from above and to the side, will remove the floor and the wall below, without getting stuck in the hole (in general, though sometimes they stupidly manage to do it for the moment).