Technically, you *could* upgrade the stereo, you'd just lose a LOT of functionality in doing so (energy consumption display, LOTS of configuration/settings/options including charging timers, all carwings functions, some options related to climate control, etc.etc.etc.etc.etc.etc....... You'd be effectively crippling much of the car's functionality.
For me, even with a relatively high-end audio build, I still chose to retain the head unit and use a line level converter. The output is actually pretty clean up to 4-5 bars from max volume (5 bars on maximized outputs like sine waves, usually 4 bars will work without clipping on normally recorded music), so if you get a nice line output converter it still gives you a reasonable signal. Doesn't fix the substandard user interface, but... well, it is what it is
Having said that, I've often wondered if a savvy developer could develop an android app and associated expansion box to interface with those functions, then connect to an android-based headset. I bet that could be made to work, though it might be a bit expensive.