Fourthmeal, very well put in your explanation. When it all comes down to it, it's the installation. Sound deadening, proper amp tuning, proper wiring and a quality built box will make the most difference.
I am actually running an OE integrator called the MTX RE-q. It is an awesome piece. It has a front L/R pre-out and subwoofer pre-out. My system sounds pretty good, however, it will never match the quality of a good aftermarket head unit.