Pregnancy: As it is right now, a Dwarf, when pregnant, goes about its business as normal, then suddenly spits out a baby. No. There is not an animal on earth, however badass, that can do that. I propose that Dwarves, when first pregnant, go about as normal. A third of the way through, they begin eating, drinking, sleeping, and breaking more. In the last third, they go 'rest' in a hospital until birth.
Families & Dwarves in the military: Could code be implemented that prevents female military Dwarves from getting pregnant as an option; "Celebate Military Dwarves on/off." When on, military Dwarves wouldn't become/get others pregnant. No need to worry about kids being dragged into battle and then having a soldier tantruming and possibly killing another Dwarf.
Hunting: I have seen a Dwarf fire a bolt into a Yak's knee, cripple it, then waste the remaining shots wounding it, and then getting more ammo to come back and find that the animal has bled out, and will not be picked up. I have several suggestions to remedy this.
1 - Dwarves get closer to prey while shooting to increase accuracy.
2 - A Dwarf that gets more ammo returns to finish off the animal it had previously attacked.
3 - A Dwarf can recognize when an animal corpse is its handiwork, and will treat it as a fresh kill (if it's still fresh).
Realgar & Orpiment: Ores of Arsenic. They're already in the game, just add in the metal and the reactions. Boom. Arsenic metal and Arsenical Bronze. Great way to get a decent, cheap metal with Copper. I've made my own code for this, as have others. It couldn't take more than five minutes, but would make Igneous/Metamorphic maps much easier to survive on.
Blood, Pus, Vomit, and other nastiness: This stuff eventually (within a month or a season, depending on the amount) dries up, flakes off, and disappears from the screen. Nobody likes having their beautiful hall messed up by a puddle of goblin blood that doesn't go away.