It would be great if the software on the ATmega8u2 had various usb "personalities" included, selectable by software on the 328.
You could send some special string to 328 to swithch it from usb-serial mode to usb-keyboard mode or usb-joystick mode.
Then, there will be no need to upload new software to the 8u2.
When power off it could return to the default usb-serial mode.