Not that i think DF is a realistic game, but it does try to model economical and logistical problems. When digging out a mountain, you are going to have an amount of stone equal to the excavation which needs to be disposed of. In the DF world this holds true currently. Id hate to see that change truthfully. What will help with this is priority mass hauling/dumping.
The ability to mass-select stone for dumping or hauling, and the ability to set the priority for that specific selection of stone would help quite a bit and still preserve the logistics of mining out a mountain. Dump/Move [Selected Stones/Stone Types] to [Specific Stockpile/Garbage Dump] with [Highest/Next-job/Standard/Lowest] priority.
A spin on that idea about Mine or Excavate and clear options would be to set a global automatic dump stones of a certain type at the lowest priority, or possibly automatically flag stones for dumping when using excavate. This would allow you to change it depending on what you were currently mining, and what you wanted to do with it.
In a way i think DF users are spoiled in that we can continue to dig, even when our corridors are filled with rubble.Realistically one needs to remove the stone and dirt before they can continue to dig further. This would create a realistic digging timetable, meaning it would take years and years to mine out fortresses that way.
It would help resolve a bunch of things people have been talking or complaining about though: Not knowing what to do with all the stone they are digging out, since it would have to be taken care of before more digging could happen. (Digging and hauling would have to be more balanced timewise.) Would also stop miners from becoming legendary so quickly, and force the player to setup camp on the surface for the first year or two before upgrading to the protection and comfort of a hole in the earth.
However i suspect that could easily be an issue for people and would need to be an option to have turned on or turned off.