For me, the military is the biggest frustration.
I'd like to think i have a good handle on the new military stuff. I can see dwarves changing from civilian to military tasks as their schedules dictate. I can see that i have appropriate weapons in my stockpiles.
Unfortunately, the little buggers like to go after enemies with training swords (when they have them), and will not pick up non-training weapons reliably. Plus, they don't seem to be able to switch weapons at all, which could be the root of the whole using the wrong weapons in combat issue.
I noticed that the ammo section lets you specify which kind of bolts to use for either training or combat. Why not have that same sort of thing for weapons in general too? Sure, they should be smart enough to switch away from a training weapon, but what if you've got them in plate and want them to use lead or some other incredibly dense weapons for training, and steel for battle?
I imagine this behavioral stuff is being worked on and we'll see improvements over the next few weeks, so i'll just content myself with getting some good initial forts designed and set up before the first wave of goblins come running in and rapes everyone with their vastly superior metal weapons and training. It certainly helps me highlight ways in which my constructed defenses can be improved.
Besides, when you reclaim a site, you get all the previous infrastructure already in place, though i did notice that the farms all had to be removed, re-irrigated and then rebuilt again, so that may be by design, or a bug. (Do they ever dry up on their own?)