I think this is more a personal preference. Also usually the supply rails are on the top and GND on the bottom, but again, I don't think they strictly need to follow the physical layout as long as the logical/net list layout is correct.
The problem I can see is that the USB connector has no GND connection?!?
I believe the order of the pins was just the order of the symbol I copied from the eagle library. Yeah no ground connection, I add it with a pour in layout. I switched to this because combining a normal pad and ground plane was a bit problematic. Could also be that I'm very good with Eagle haha.