The idea was to align the Ethernet port with the USB port, on the outer side of the board. Originally I designed the PCB to be the same size as the Protoshield (still not as large as the full Arduino board), but it could have been a little bit better... but I saw a lot of empty PCB space and it looked much better a smaller board.
Maybe for Version 2...
well I have an idea how to fix this for version 2. photoshopped
I could lay it out if you supply the schematic
Split the board in 1/2 and use right angle headers and use a simple wire to connect the 1/2s together
there is plenty of space for everything