I think we really need only one thing: A 'clearing' job that has dwarves clear away rocks (or other items) that are in the way of construction, blocking major passages, and so forth by moving them to a stockpile. Whenever a floor plan is dropped, any untagged items on the floor that would cause problems for it get clear jobs set on them... Any items left in a doorway would get automatic clear jobs. If too many dwarves walk over an item in a short time period and it's just lying on the floor outside of a stockpile, it could also get a clear job.
With this, stone wouldn't be such a big problem... dwarves would clean it up when it's in the way without having to worry about all the stone in distant mines.
I would really rather not see anything done that reduces the rock supply. I don't know what other people are doing, but I've run out of rocks almost as often as I've run low on wood. I've been forced to shave the front of the cliff and dig out large lines just to get enough rocks to keep going.
...I should mention that I have two craftsmen doing rock/wood crafts and one mason churning out doors, blocks, tables, thrones, and other items at all times. And, also, I have covered huge portions of my fortress with rock-fall traps, built numerous rock bridges, and used rocks most of the workshops I produce. But this is partially because I know I can always get more so easily...
I think you people just aren't taking advantage of the things you can do with rocks. Rock-fall traps are a decent and easy defense; putting a coffer and a cabinet in each dwarf's room is going to be helpful later on. Putting a masterwork table and chair in each will help keep dwarves happy even more. Your halls should have rock doors everywhere, since they provide a little security, will protect you a bit against nasty things like floods and miasmas, and can be used to lock off insane or tantruming dwarves.