This is how should look. But here are few issues:
1. - Digital 13 pin and Aref pin on extension sockets are not connected. Solution: I really don't care about them because I don't have other free pins left :-P;
2. - 3.3 pin from extension sockets is unconnected. Solution: this is an important issue because you can't use the existing Arduino shields which require 3.3 volts. I will place a via close to it, allowing you to connect an LM3940 which can be mounted on a little extension board or sticked on the board with glue (for your own shields, you can mount it right there, on shield);
3. - The ICSP male connector is too close to USB-B connector so you can't connect your Pickit2 programmer directly. Solution: I will use a female connector, using two male connectors with wires as a bridge between the board and programmer.
4. - When you connect the board to USB or Pickit2 programmer and jumper is set to internal power select (and no external power connected), your shield don't have power. This is an intended issue. The board don't have protection for USB power and is wise (and required) to extract your shield when you program your board with Pickit2. Always use external power when you program the board (or exchange data) via USB and have the shield connected. On short version, a shield is powered only by an external power source.
Of course, the board can be resized to make room for all components but I don't want to do it. I like it as it is! Remember, no SMD components, easy to build and close to Arduino board shape. Anything too big and different from Arduino board shape will render the board less attractive. Anyway, is good enough for the first version...
Anyone can manufacture it with SMD components for commercial if have the possibilities.