tim7:
It would be better to keep the DFU bootloader, to make subsequent reprogramming easier. I don't have an Uno R3 (yet), but I'll look into it.
I have a Arduino UNO R3 (clone by EKitsZone). I self has interested to create ISP-programmer interface based on mega16u2. Simultaneously, these i did not want to lose the use of DFU. Memory size of 16u2 should allow cram two program block (serial&isp + dfu). I had to cast with source code, him compiling and tuning ... The result can offer a ready-made firmware for 16u2 - use please ... http://files.migera.ru/arduino/isp/16u2-uno-r3-dfu-isp.hex
PS. Burn to 16u2 through usbasp (example) and avrdude ...