it seems like the holy grail would be to get a small AVR onboard that could emulate and appear to your computer as a USB<->serial adaptor. no HID stuff, no funny business. just emulate the FTDI chip completely.
Emulating the FTDI chip is a massive undertaking and likely fraught with technical and legal trouble, but CDC virtual comports are a reality right now for AVR-USB, the best known implementation is
AVR-CDC. It's sometimes sketchy, but after tweaking the latest version I've found it stable-enough for hobbiest kits.
is this possible? how much work is required?
Is it possible, yes. You'd need an AVR with a hardware UART and atleast 4K of flash. What we really need is for atmel to invent an ATtiny4313. For now, with an ATMega48, this should be doable, but you'd need to dedicate enough space for a second DIP28 device. Additionally, currently AVR-CDC doesn't work on Vista or modern Linux kernels (without patching).