As an alternative, if you want to use standard proto/strip boards, with standard header pins/sockets,
you can buy third party boards that have an additional set of holes.
This gives you both the "Arduino" offsets as well as standard offsets if you solder
in another header.
The Seeeduino is an example of such a board:http://www.seeedstudio.com/depot/seeeduino-v221-atmega-328p-p-669.html
The Arduino team rejected this idea as they claimed it ruined the beauty of the board
and that the board with its flaw represents the natural flaws in all things.