Well, not that most of that is a problem for quarries. But you still have the issue that stone weights a *lot* more then wood, by volume, so it's much more difficult to create buildings out of. Wood can also be easily nailed together, even with wooden pegs, and it is easy to see why wood is preferred over stone, or even brick, everywhere that has ample supplies of it. It's only the more well-to-do that have stone or brick houses in those cases, since they can afford to hire the additional labor to make the houses quickly.
Yeah, good catch on me conflating open-pit mining with subsurface mining. And yeah, the construction process should have many more difficulties beyond just obtaining the raw materials. You probably shouldn't be able to build an unmortared wall of rough stone more than a single Z-level high.
Well, if mining became too difficult then that would take a lot of fun out of the game. Imagine trying to dig into the mountain side, and not three tiles in the cave collapses and your miner dies.
You could say that about the current version too -- if you ignore the warnings and dig into a magma pipe, your miner will probably die. Obviously additional difficulties wouldn't be implemented without new ways of dealing with them, or at least avoiding them. I mean, take your collapse situation -- that's not too far off from what could happen in the 2D version, and the game still contains a mostly obsolete building designed to avert collapses. So we're not talking an unprecedented increase in difficulty here.