I have a different perspective on audio. The factory upgraded system is one of the best I've ever heard. So hear me out...
I'm a big fan of "staging" and tonality. Basically, there's a response curve that people like or don't. But overall, when people hear something different, it's typically attributed to "better". There's a lot of science and white papers to help understand psychoacoustics and how our brains interpret sound. But basically, whatever is heard within 20ms of the initial sound, is averaged together by our brain. Beyond that time frame, your brain will ignore it. So anyways...everything in your car is within that time frame. We aren't hearing JUST the speakers. We're hearing the speakers PLUS the vehicle itself. So in order to gain staging and tonality you need to correct/counter the response of the speakers+vehicle. A well recorded stereo image will allow you to identify and locate where the singer, instruments, or other aspects. You lose that with poor response.
Why did you just read that? The ONLY way to "correct" your vehicle response is through equalization. There's some other tricks too, like time and phase alignment but our factory radios don't utilize anything like that. But it does use equalization. That's what you guys are turning off.
If you like it...that's great. No big deal. What do you lose with it off? You lose "up front bass". When your mids and subwoofer are properly level matched and play together, you'll NEVER KNOW you have a subwoofer in the vehicle due to how your brain perceives those wave lengths. BUT, you will get a nice bass line out of it. However, with it level matched, you perceive as loud as it actually plays. You also lose coherency since the midrange is all over the place. You won't notice that as much unless you have hearing damage. Those are the two biggest issues for me. And what do you gain?...well all cars are bass machines. Without the corrected sub levels you get more output, good or bad. You also get more distortion...Distortion interpreted by the brain = loud. So with more distortion you'll assume it's MUCH louder, whether it's the subwoofer or another driver. Distortion can also be painful. So really, sometimes you want distortion to keep you from playing the volume too loud(protecting your ears)
What happens when you have a finely tuned system? You won't know how loud it is until you have to scream at the person next to you

You also won't know there's a subwoofer in the trunk or wherever you placed it. I've had many people believe I had a subwoofer in my engine bay until I physically displayed it in the trunk YET they still perceived it up front.
Alright, enough blabbing. I enjoyed the factory setup. It needs a few things but turning off the pre-measured EQ didn't do anything for me. For reference, here's what happens to speakers in a vehicle when left uncorrected...
If I get time there's a chance I'll start doing some car audio upgrades. In the mean time, feel free to PM any questions if you'd like