About the shield issue... if its a concern that 5v shields would be used with this board and the solution is to change the pin spacing of the headers to force a new 3v shield design then I just have to ask whats the point of sticking with the arduino footprint?
If you plan to change the headers then just go ahead and shrink the board size and introduce a couple new smaller shield designs. I do like the idea of the lipo friendly factor. I think in the interest of ultraportability then just go ahead and make it smaller!
I have had this issue with the lilypad and now this board, your programming header doesnt really stick with any sort of standard. If you had the 6pin ftdi compatible pinout (look at lemore's boarduino or paul's bare bones) then your customers would have more options for programming adapters and you could enable the auto reset function in your designs.
Finally since this seems to be about options, I would add 2 pins at .1" spacing for + and - at the power connector to allow for some male pin headers to be soldered by the user instead of a barrel connector. This could be under the barrel connector or to its side somehow. If done well, the large holes for the bigger connector could be used as strain relief if soldering in wires.
And which vreg did you use? If it is indeed only good for 40mA then that really needs to be noted.
Make it smaller!
-Brian