This is why I don't see the advantage of doing all the work to implement a bus protocol, when USB functionality costs nothing more than an FTDI chip ($3-4).
True, but if you put an FTDI USB chip on every daughterboard (is this what you propose?), how do you connect it to the FPGA? Here you still need I2C, SPI or JTAG. Then you can also put it directly on the backplane and connect the daughterboards only using i.e. I2C. USB on the daughterboard will probably also require more careful routing and special impedance matched connectors because it is a high speed bus.