I changed the design again >_<
The main reasons for the change are not wanting to have to drill lots of holes in the cases and wanting to reduce the amount of external components required to support certain controllers. You can now plug Neo Geo pads in directly thanks to having both 9 pin and 15 pin connectors. Having a 15 pin connector makes supporting things like PC Gameport devices easier too.
The AVR has been upgraded to an ATmega168. 16k flash ROM and room for a boot loader, so firmware updates are possible over USB. There are also more I/O pins available.
Finally, the USB port has been done away with in favour of a captured cable. The USB spec says you must have a captured cable for USB 1 devices anyway, and now a USB port won’t easily fit. Since the cable is flexible it also means drilling holes is a lot easier as they don’t have to be exact. The only potential issue I can foresee is strain relief.
Seeed Studio is doing a special offer with 30% off, so I’m getting prototypes made up.