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.
Thanks for the suggestion!
[1]: http://www.reddit.com/r/arduino/comments/2ehosj/pcieduino_fe...