O_Shovah, I'm sorry to derail the thread. I think Salzgitter had a great idea:
One other idea: if you plan to put an USB port onto every doughter card, wouldn't it be easyer, to forget about all that SPI and I2C busses and just route the individual USB conectors of the FPGA boards to an USB hub onto the backpane, which will than connect to the host PC by only one USB port?
If we wanted to add ethernet to the motherboard later, this would mean adding a MCU that could serve as a USB host.
USB has my vote.