There are a lot of aspects of this game that I think need more player control.
1) crafting. There need to be toggles you can set to mark specific materials for only specific tasks. For example, there needs to be a way to flag Bauxite for use in mechanisms only; there needs to be a way to tell your stonecrafter to only use Obsidian (or to not use Obsidian, if you're saving it for swords). You can sortof kludge around this with stockpiles but it's awkward, inconvenient, and unreliable.
As a sub-issue here, I'd like a toggle I could set to "use best available materials for artifacts." I'd like to be able to save my platinum bars and dragon bones for awesome artifacts, and not have everything just be Orthoclase Earring, Decorated with bands of Rhesus Macaque Bone.
2) It'd be nice if you could set a skill level for doing engravings. I only want legendary engravers doing engravings, not my army of floor-smoothers. As it is I have to turn each one off manually . . .
3) Army. There needs to be a more precise level of control over the military. Specifically:
a) You need to be able to set dwarves to use the best quality weapons available when on duty and the worst quality weapons available when sparring. Again, you can kludge around this with stockpiles but it's incredibly awkward.
b) Fortress Guard and Royal Guard. The only purpose these serve is as a retirement group for your cripples, and the reason is that players have no control over dwarves in these groups. That's not a good thing. Maybe make dwarves in these groups have priority for the best gear, or have extra happy thoughts, but don't take control of these dwarves away from players. If nothing else, I really like to maintain careful control over who's sparring when, due to danger of spinal injuries, and the royal guard can screw that up, well, royally.
c) this may be a bug -- i think it's derived from patrolling and last remaining orders -- but i've had a real problem at times getting dwarves to NOT charge the goblin seige solo and instead obeying the "dwarves stay inside' orders.
4) More of an interface issue, but i'd really like a better way to scroll through and select items for melting, dumping, etc. It'd be really nice if I could quickly select, say, all non-masterwork armor for melting, or all narrow armor, without having to scroll through 1,000 pig tail socks in the process.
On a similar note I'd like to be able to turn off job cancellations in shops (just wait till they finish smelting the bars, dammit).