Well, when its just for density, I'd rather take a wooden board and cut some grooves ontop of it, gives me a place to put the FPGA boards for free.

Please, dont get me wrong here, I really like the whole idea of a modular assembly, but I just can't see the point in making a backpane that just serves as a mechanical mounting platform.

On 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?