I don't know what the "base" stero was, but if it's working well for you, I'd leave it, unless you want to go to an aftermarket. My '03 has had 2 radios and 2 cd changers replaced and they have to be replaced again. The cd changer is screwed and the AMFM has terrible sound. It is the Bose system and if I ever get another cad, or any other car it won't have that system in it-EVER
If you're talking about the head unit (radio) that has little to do with the 'Bose'. Bose refers to the amplifier in the trunk and the speakers. Replacing the amp would be a bear, as it has a completely different wire harness. The speakers are also different impedance, and include a center channel speaker in the dash. The Bose sub is a single coil, and the base is a dual coil speaker. The Bose amp also has some inputs for audible directions when paired with a Nav.
I don't know if the base head unit had a six disk changer, but if not, that would be the main advantage. The head units are completely interchangeable.