I'll have to look at them in more detail, but compared to your previous prototype boards, in addition to my previous complaint (in email) about stackable headers which is addressed in the boards with offset headers (or as you mention female headers), the top side silk screening did not indicate which pins are connected to which. As I was looking at it, I had to keep flipping the board over to make sure I had the alignment correct. Please have the silk screening indicate what pins are connected to what, particularly as you will soon have several different board layouts.
The previous boards are to be updated with top-side silk screening of the connections, bottom side identification of the pins and the new shape. We also added a link to the stackable headers from the web page for ordering the previous boards.
I also did a circuit continuity test, and the two power rails down the middle aren't connected to ground or 5v. Now obviously, that can be more flexible, but I suspect it will be friendlier to people like me moving from breadboard to prototype shield (or use other prototype shields that do connect the rails) if the connections are made.
There are too many possible configurations for the power rails to make it generally beneficial to connect them to one power pin or another. On the Adruino, there are 3 choices (5V, 3.3V and Vin) and then there is the possibility of external power, two voltages and no ground connected via wires, which side should be power and which side ground, or even using them for something else besides power.