Most times people decide to get a different radio because the factory radio cannot be modified or lacks such functionalities like the USB port. I have both radios on but I never use the factory radio. Seems a bit cumbersome to operate both, if you ask me.
The one in my car had everything that I wanted. I've got the Ford Expedition, and the radio works perfectly fine like I want, but I get your point that it can be cumbersome running two car radios in the same car.