I'll jump in on the other side: I do not like the sound of replacing the FTDI with an HID.
With the FTDI USB/232 device we've got a simple device with a simple interface and a company that supports the drivers on all platforms. If the FTDI is replaced with an AVR-HID, then we've got the HID drivers to worry about, which means that someone (the Arduino developers, unless someone else steps up) must tackle USB device driver development for multiple platforms (linux, Mac OS X, windoze).
AVR-HID sounds like a good way to lose cross-platform support and reliability.
The only real reason to replace the FTDI with an AVR-HID is to use the AVR-HID as an in-circuit programmer (thereby saving the bootloader flash space), but that could be done by just requiring an Atmel device for US$34, and make the AVR-HID a completely separate project.
IMO it works fine, the price is reasonable, so leave it the way it is.
-j