OEM audio systems have progressed to a point that after-market systems have lost a lot of their appeal. Many of these systems are now so intigrated into the vehicle, that they are no longer referred to as "Audio System" but as "Infotainment Systems". The after-market is targetting the boom-boom crowd almost exclusively as that is who is buying those systems now. Accurate high-fidelity is in the OEM domain now-a-days.
The automotive environment sucks. Accoutically you would think that since you have a defined space, it should be easy, but it isn't. Nothing about the vehicle interior is condusive to quality audio. As I've mentioned in previous posts, I have been designing amplifiers for a major premium OEM for almost 20 years now. I can tell you there is some serious processing going on to tune a system properly, from the electronics side. And the mechanical and enclosure aspect is no less regorous.
There are a lot of quality after-market head units out there. But speakers are a different story. There are components available that can work in an infinate baffle, but that comes with a LOT of sonic compromize. A properly tuned enclosure can help reduce the need for extensive processing (but not eliminate it).
Adding a quality EQ can go a long way to helping. But do not tune it with a pro-audio mind set. You will need to be far more aggressive than that. And pay particular attention to the phase response. You would be amazed at how much energy is completely wasted to cancellations.