First of all: I love the tinkerer kits!
Still, as the nitpicker that I am there some things that might be improved in future releases.
The soldering pads on the double headers might be a bit bigger.
I think that all the pins that is broken out from the “Arduino” headers should have the same markings on the base board.
I would love to have a ground, 5V rail across the proto area (like a breadboard).
The soldering pads on the prototyping area should be larger and the silk mask in my opinion is misleading (se the image). To me it seems that the pads are grouped in two, but they are actually just single non connected pads?!