I want to say animals have been fixed, at least with what merchants bring to you, but I believe the quirks with them being traded by you are going to be resolved in .13, which should be out pretty soon based on the bug tracker. There's something like 19 fixes coming up, including all of the major ones involving trade.
It's a little tougher to design fortresses, imo, these days because of the caverns; depending on the depth of your map, you might break in to them too early and wind up throwing off your fortresses' entire design. Mountains are generally safer in this regard since they have more z-levels above ground. However, some of the caverns you can get are pretty amazing on their own and building a fort in them can be a major aesthetic achievement if you're careful. I for one usually aim for a mix of pragmatism and realism in order to make my forts look more like settlements.
Steel is pretty much now the incomparable leader of the common materials, although I've heard that silver is of course good for warhammers due to its density (although I generally use steel myself). It'll deal with anything else except steel/adamantine quite well, but a challenge is that the armor system still makes it possible for weaker blunt weapons like copper maces to inflict damage on armored targets. The only creature I've had trouble dealing with is the bronze colossus because of the nature by which it's killed (presumably I needed more spears and battle axes). I believe ranged attacks are also still pretty ridiculous, although this can be mitigated by good armor layers.