Mining is a mindless task that has been made more and more frustrating over time, but in ways I can see acceptable. However, arguably one of the WORST parts of finding the mother lode comes after mining everything one by one, dodging cave slimes and dying pillars, and stockpiling everything together.
The worst part is transporting all of it to the surface, because the best method you can use is carts filled with wheelbarrows. You can build a wagon, but wagons can't go up and down mineholes, so eventually you'll be stuck with a cart anyways (even if just used to bring the wheelbarrows up to another wagon)
Thus, I propose another addition to the "machinery" system: A rope and pulley excavation structure. The structure should be built inside a building OR as an expansion to the mine hole structure. It should be able to hold a large amount of objects (that is, wheelbarrows), or just serve as a VERY LARGE stockpile. You can only function with it while the 'lift' is on your level, and you can right click the structure to 'pull' the lift up/down to the level you're on.
This would serve as single structure that can reach down to as many connected mineholes/connected floors (if its a building, presumably it would create additional 'holes' in the ground in the layers beneath), of which you could bring ore and stones to for faster transport to the surface.