Having to irrigate soil to be able to farm, dwarves working until they get bad thoughts from being dehydrated and starved, meat and such not fit for eating or making meals. (I resolved all three by setting my dwarves to noeat and nodrink. Call me a cheat, but having constantly unhappy dwarves isn't better).
Hunters not hunting at all. (Resolved by designating the entire outside layer as a single burrow and have 5 dwarves decked out with steel swards and plate beat the sht out of anything that moves).
Military dwarves either not training at all or they do indeed train but with useless results. (Resolved by those dwarves being stationed outside and just beating unicorns, instant legendary skills).
Caverns. Sorry, i know a lot of people love them and they're a nice idea, but personally I just find them annoying. I ignore them for the most part, rewalling every entrance I accidentally open and dig around them.
Military dwarves running around with two weapons in the same hand and of course only using the training one. (Resolved by just designating those training weapons to be dumped in stocks screen).
Trees and bushes growing like crazy on my soil layers after I found a cavern (without the soil being irrigated, mind you).
No good way to differentiate between bones/shell/skulls and other refuse. I designated a stockpile inside close to the butcher's shop only for body parts and the remaining refuse goes to a stockpile outside. That helps a little, but there's still a lot of useless junk lying around there. Not to mention the never rotting corpses and remains outside now. And the blood.... arrgh.
Think that was all. Very nice release alltogether, but needs a bit of working