Now days, the factory sound systems have improved dramatically. Some are actually pretty good. I still haven't heard a factory car stereo with good bass, most are boomy/mushy sounding. I guess that's probably what most people expect. But it's better than the nasty stuff kids put in their boom-boom cars.

You want the best? Get a good head unit and a good amp. Then focus on the speakers. Build speakers yourself with high-quality, high-efficiency drivers like JBL Professional Series, TAD, B&C or Eminence. Design the bass cabinet for response that's overdamped so cabin gain congugates it for deep extended flat response that isn't boomy. With speakers like that, you won't need much power. Fifty or one hundred watts is plenty. That will give you the best quality sound system you can have in a car.