why do the basic microprossessor boards from all vendors that I've seen not utilize headers that have pins sticking out the bottom
Mostly I suspect because they would be vulnerable to mechanical damage and subject to shorting out on everything you place the board on. That said a board I've designed has the headers "upside down" with the socket part under the board. That allows stacking in both directions and also allows for different stacking heights to clear tall components, something you can't do with the socket strips in the normal orientation.
easy for individuals to fix by just desoldering the existing headers
Ever tried desoldering a large header, not easy unless you destroy it.
Where can I get a breadboard with pin spacing specifically designed for an Arduino shield?
You won't, mostly because they stuffed up the design and the headers are not on a .1" pitch.
It would be very convenient if there were a row of holes outside of the vertical headers that were elecricly connected to the header pin beside it.
Very true, and I think I have see a board or two with that feature.
A stack of shields can only have one "top",
True, the only practical way I can see is that the top shield has to do all
the HMI stuff.
Perhaps some sort of three dimensional cube arrangement
Not quite that but the Tower system http://www.freescale.com/webapp/sps/site/homepage.jsp?code=TOWER_HOME&fsrch=1&sr=3
has a display module that plugs onto the sidehttp://www.freescale.com/webapp/sps/site/prod_summary.jsp?code=TWR-LCD&fsrch=1&sr=17