arduino design question...

I still think it should be fixed someday instead of having be considered to be "quirky cuteness".

That's been discussed a lot in the past and the consensus is that too much hardware would break as old shields would then not mate with the 'newer' standard boards.

Some vendors have come up with a nice compromise in that they put additional pads for a proper spaced connector next to the existing connector. If you populate it then you could utilize a shield using standard general purpose multipurpose material that utilizes standard .1" spacings.
Here is one example:

http://www.seeedstudio.com/depot/seeeduino-v328-fully-assembledatmega-328-p-439.html?zenid=9f6118c193cee9f8b7337d4df91a2eca

Lefty