First off, I'm sorry if this is a perennial topic; I tried searching for similar topics, but I wasn't sure what terms to use.
Anyway, it's currently rather well-documented just how much of a drag it is to have stone lying around all over the place. Whenever you dig anything out of rock, you leave behind a vast array of regularly-sized boulders, which clogs your stocks screen, uglifies the fortress unless you hide it or dump it, takes up space you might want to use for stockpiles, etc.
I realize that this is an attempt to model real-world mining; however, unless you are actively quarrying a type of rock, you wouldn't typically end up with usable chunks. (I assume, at least. I know less about mining than I do about, well, almost anything else.)
So basically, what I'm proposing is that there be two different digging styles. One could be simple "digging," which would not leave behind boulders of usable rock, and which would leave a coating of waste rock and dust on the floor. Since waste rock isn't exactly easy to traverse, it would be important to clear the area of waste rock in a process similar to smoothing. This would *eliminate* the waste rock completely; no boulders, pebbles, or any sort of item would be left behind. Paths covered in waste rock might take more time to walk through; rooms that have uncleared waste rock on the floors may cause unhappy thoughts (He stubbed his toe on a jagged rock chunk lately), and floors that have uncleared waste rock on them would not be able to be smoothed and engraved until the rock was removed. The labor wouldn't be lengthy or time-consuming, though, and maybe could be on by default for all dwarves, like hauling. The "digging" style would take about as much time as the current mining labor, perhaps a bit faster.
The other would be "mining," which would pretty much be what we have now, except perhaps a little bit slower to show that care is being taken to extract usable chunks of stone, boulders, etc. Ore would be automatically "mined" rather than "dug," as would economic stone (except for flux if it makes up the whole layer) and gems. Perhaps certain rare clusters like petrified wood or pitchblende might be automatically mined as well (maybe the player could set mining preferences to always mine rather than dig certain types of stone?) Removal of waste rock would not be necessary in "mined" passages, but it would leave behind boulders, gems, etc.
I think this is potentially a solution to many problems; it would potentially raise FPS by having fewer items on the map, would allow large stockpile areas to be dug in stone layers without needing to haul stone out, would make stone a resource to be managed like wood or metal (unless you want to mine everything anyway), and would reduce the annoyance factor for digging new chambers in the stone significantly. It might also make stone stockpiles *practical* instead of completely unnecessary (although quantum stockpiling is probably still going to be the norm).
Anyway, that's my idea; feel free to mercilessly tear it to shreds, at your leisure.