The stone management is a problem, though it's not a big one. The problem is that whenever someone gets a job that requires stone, they always seem to pick the one that is FARTHEST away from them. It would be nice if I could specifically zone mining to have the stones be automatically forbidden. Or to not leave stones, but that might be asking too much.
What I'd like to see is when a dwarf picks a stone for a task, and paths to it, as they're walking the path, they'd check within line if site (either their current square, or 1 square in each direction), and if there is an untasked stone, use that instead.
This could also solve the problem of the dwarves going out of their way to go get the stone 1 or 2 z-levels from them, if the path they'd take would take them past a stockpile or other untasked stone. (one slight performance optimization, at the cost of memory, would be to store the expected path length, and then only site-check stones once you've gone further than that length (since if there were a stone within that length, the dwarf probably should have chosen that one anyway).
I think it could add a bit of realism, as well. I don't think we'll ever get away from telepathic dwarves (who know that stone is available the instant the dwarf 20 z-levels below them mines it), but I think it'd be nice if dwarves headed for the nearest stone stockpile when they need stone, and grabbed one if they happened to see it along the way. Could mean that dwarf then carries stone a lot farther than need be (slowing him/her down a bit), but the exercise would do them good.