Hi,

I don't know too much about hardware, but I still want to comment on a few points:

1.) Power connector: I hate those molex-connectors but the ability to use a standard ATX PSU without hard-to-get adapters is worth going with it. But I also think that an ATX supply isn't the most efficient choice, when you use only the 12V rails. Also they are rather expensive, usually overpowered and need active cooling.

My suggestion: there are a lot of aftermarket notebook power-supplies, from very cheap (http://www.amazon.com/Notebook-Charger-Adapter-Thinkpad-40Y7659/dp/B002BW0MNU/ref=sr_1_1?ie=UTF8&qid=1309117838&sr=8-1 or http://www.amazon.com/Replacement-Notebook-Adapter-Charger-Inspiron/dp/B004FQPGG8/ref=sr_1_4?ie=UTF8&qid=1309117838&sr=8-4) to better ones with higher efficiency. Cheaper, passively cooled, still enough power. Adding such a connector and a 12V regulation to the motherboard might not be too expensive?

2.) Onboard controller: I like those embedded ARM/MIPS-CPUs but I think they shouldn't be on the motherboard if they are not necessary. If the USB-bandwith is enough to supply all those FPGA with data, then leave the high-complexity tasks to the Host. And it really doesn't have to be a PC. I have a Sheeva Plug which takes less than 5W and has a 1GHz ARM with 512MB RAM. More than enough I think.

3.)

Since you can't power the whole FPGA-array through one USB-port and we will need an external power-supply anyway, I'd suggest to also power the FT2232 from the power supply. Why? There are potential host-devices that can't even handle the minimum 100mA. For example an Android phone with a modified kernel to support host-mode ... would also be a very power-efficient host.