I have a 2001 Bonneville SE. I was told all the same stories. I have replaced all of the OEM audio equipment with aftermarket. I used a Scosche wiring harness and install kit. The only problems I experienced were that the accessary wire (red) was not an accessary wire (didn't do anything at all), the install kit barely fit and I lost my door chime.
To fix the accessary wire problem, I had to splice into the ignition wire behind the steering wheel.. (not difficult if you know what your doing)
By removing the brown dimmer wires from the harness and detaching the OEM harness and antenna plug from the clips inside the back of the dash where the OEM radio plugged into, made just enough space to install the aftermarket DEH-P6300. Still a tight fit, but it looks good.