This is starting to sound like a broken record, but definitely the training bugs.
One peasant came in with no skills but novice crutch-walker and novice conversationalist, but incredible physical stats. So I immediately assign him to the military, but he has never stepped into the training barracks, and after the most recent siege is unhappy, with "complained about the draft recently," on his thoughts screen.
Axeforgebeard: I've only made two 0.31 forts, but both got along fine with setting my dwarves to use the default leather uniform, then switching it to the default metal uniform.
Admittedly, the interface for making that switch is pretty painful. And it'd be nice if they'd more often go for the *steel breastplate*s, minty fresh from the forge, instead of the <copper mail>, shucked off a dead goblin.
I also really really can't wait for the improved, more realistic irrigation system. I apparently washed away a bunch of the mud in my farm room while irrigating it the first time, and those ugly patch work farms taking up only half of my farm rooms really grind my gears.
It'd also be nice to be able to plant surface plants in mud. Having to find a place to dig an area near the surface of my half-rocky mountainous region, just to get a little more variety, is pretty annoying.
Some of my dwarves are unhappy after spending the night in a poor room, or being disturbed by noise. None of their quarters are poor, and the living arrangements are far away from the main work areas. They're all stone, and typically have a + or * coffer, cabinet, door, and bed. But for some reason, they all love to stop off and take a nap right in the half-soil hospital, dug out near the surface, with siege engines above and workshops below.