I think you all should try to keep it simple. That increases chances to produce something that is working in time and without multiple iterations for PCB production and assembly (money!). The later this thing is ready probably the higher is mining difficulty, this in the end also costs money.

As far as I can tell USB is a much more complex protocol than SPI or I2C. Thats why FTDI can sell chips. Implementing USB inside the FPGA costs LE cells that could otherwise be used for mining. In addition there is a host needed to connect multiple slaves. For mining no bandwidth is needed. SPI, I2C, JTAG all are capable of pushing enough bits for mining.

My proposal:

• make the motherboard simple, put only the FPGA + decoupling + one of (SPI, I2C, JTAG), put an direct JTAG connector on the board for debugging the FPGA.
  
• let the motherboard supply one of (SPI, I2C, JTAG) + programmable power supply + reference clock. Power needs cooling and you normally don't want to have this on the daughterboard. Connect the motherboard to a standard PC power supply.
  
• The simplest motherboard would then just put an FTDI USB connector on the motherboard and you are ready to go. Easy debugging. Anybody who feels up to the task can then replace it in a second step with a microcontroller and ethernet.
  

We build a similar board (not for mining) at work and you will find out that it is a pretty complex task. You will succeed much faster if you try to keep complexity as low as possible.

And just as a reminder: to my knowledge there is at least one startup working on an ASIC, announced to be ready in October. If this is true, an FPGA board only suitable for mining will be worthless.