What I understand from reading the press release, the USB enabled AVR is just going to replicate the functions of the FDTI, ie act as a USB to Uart bridge. But since Arduino now has it's own USB hardware ID, it can show up on the USB bus as an Arduino, instead of a com port. But they needed something else to be able to transmit the ID, since a FDTI has it's own, and can't be changed. The Uno will require Arduino IDE v20, which isn't out yet.
So really, besides they upgrade on the MEGA, there's nothing new here except branding. Now even the computer will know it has been blessed by having an Arduino plugged into it.