Hi Neil, welcome to the forum. Our board is too close to production for any hardware changes at this point, and even seemingly small changes do require a great deal of time to fully implement, so the hardware is definitely fixed for this generation. However if this one is successful there could be a Mk II someday, but not for several years.
All the same I'd be interested to hear what chip your group went with. If it is the MCP2220/MCP2221 then I did consider those, one thing they did not have is the ability to pass the DTR signal. This is not needed for pure USB communications but the Arduino environment is unique in that it uses DTR to reset the device for flashing.
But you are right the PICs are certainly less expensive and that is one of the drawbacks of the FTDI. On our board the FTDI is the 3rd most expensive component, after the processor and the L298 dual motor driver.