Hmm, not sure whether I should get a vote or not. I've only really tried to play once, and I never made it to the endgame -- so there are probably tons of things I have never experienced or noticed or discovered. But I DID survive for a few years and ended up with almost 90 dwarfs before the Bad Things happened.. . :-)
So I'll limit myself to thinking about the gameplay mechanics, as opposed to the actual game world content. After all, I haven't experienced so much of the current content -- so I wouldn't really know what's missing and what I just haven't found yet. Having said all that, my vote goes to...
1 - Improved interface for Construction. Especially for walls and floors, it'd be great if you could just pick the corners like when designating an area for digging. Ideally, you should also be able to pick the source material only once for the whole construction -- Building a large floor out of the same kind of stone is a huge pain right now when you have 20+ different materials to choose from.
2 - Inventory control. When viewing a dwarf's inventory, it'd be nice to be able to scroll down the list, find that nasty old xRusty Old Swordx, hit R)eplace, then scroll down the list of all currently available items of that type (e.g. Weapons) or for that slot (e.g. Held in Hand), and pick out the *Vorpal Blade of Devouring*. As an alternative, allow items to be assigned to individual dwarves similarly to the way rooms (tables/chairs/beds) are. Then I could just go through my stockpile, find the *Vorpal Blade of Devouring*, and choose to give it to the dwarf of my choice -- after which s/he would take "Pickup Equipment" as a task in the hopefully very near future.
3 - Clutter control. My dwarves tend to drop their old belongings all over the place, even though I give them nice furniture to put it all in. Maybe when you get the Manager, there could be an option to order all dwarve to "clean up belonging"? Or, alternatively, add an interface option for changing/removing ownership of items so you can D)ump those items. Or letting items be set as either Forbidden, Owned, or Free.
Anyway, those are some of my thoughts. I have many others, but I think we only get to vote on three, right? :-)