The male headers are very useful when using servo's, but for the other headers it looks to me if it would have been safer if you used female headers (as Arduino has).
I chose male headers because all of my servos and sensors ( like the Sharp IR and PING) have female connectors. With all male headers I could plug in all my servos and sensors without any hassle - no extra boards like I would need on the Arduino.
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Wow, nice one. Really looks like a good Arduino clone, and I like these 'more specific needs' Arduinos (as in this one is designed for robotics, another for something else, etc.).