not sure, but shouldn't you be able to use the ATMEGA32U4-AU as the microcontroller and get usb for free? Here's a good place to start for a bootloader that'll do your usb setup for you... http://forum.arduino.cc/index.php?topic=124459.15
Just looked at your product idea, see you already had planned a good microcontroller. Maybe replace the FTDI with the ATMEGA and make a firmware that'll allow in circuit programming so you really can't brick the main microcontroller?
Yeah, people suggested something similar before[1], and definitely will research it. Using two of the ATmegas might not work (the miniPCIe form factor is tiny!), I wonder if a single chip could do that, at the expense of maybe some storage? The current setup needs almost no custom work, and for the proof-of-concept version I'd rather not do firmware programming if I can avoid it (but then maybe I can't be picky about the FTDI:)
Look at the datasheet, it's got a usb DFU bootloader loaded by default. :) Biggest issue would just be making sure it can switch over to serial mode, but that's already done in arduino's, so should be pretty easy.
