I approached the issue in stages and measured the performance improvement of each step. Here is what I did.
1) the stock speakers are crap. I replaced the front with Infinity 6030cs and the rear with JBL 622's, cutting adapter donuts out of 3/4 MDF and mounting the 1" domes in the front doors by cutting a circle in the existing grills. The improvement is very significant. These high efficiency low impedance speakers make the most of the power that is there. Many people would say this is good enough, but not for an old rocker like me.
2) I used an audio sweep generator and rms voltmeter to measure the effect of the HU built-in EQ. This is what the cleansweep and other automatic equalizers do, but it is only half of the job. This process does not measure the acoustic parameters of the speakers or the environment. One can remove the factory EQ which in the case of my Pioneer/Toyota nav was mainly a big boost in the bass and a small one in the midrange, but it takes a sound level meter with the sweep generator to measure the system performance.
3) I added a Soundstream Rubicon 600 (150w rms x4) and put it in the tray behind the back seat, along with a Sony 500w sub amp for the Pioneer TSW-841D I put into the back door. The amp has built in HP and LP filters that I was able to use to remove much of the stock EQ, and in combination with the on-screen tone controls it was a huge improvement. The amps have speaker level inputs. It sounds great but not quite there yet.
4) I decided to put in a pair of parametric equalizers so I could have separate EQ for the front and rear and preserve the on-screen balance control. To do this I needed to convert the balanced speaker signal to the unbalanced RCA inputs of the Pyle 520P units I am modifying today to fit in the space below the HU. I tested the Scosche unit and the performance at low frequencies is terrible. The PAC converters are the same price and are literally 100x better at 20-100Hz.
The Pyle units are half DIN, and the space is almost wide enough but not quite. I could remove the plastic shell; there is lots of room around it, but I decided instead to take the EQ units' PCB's out of the case and whittle them down in the rear as much as the boards allowed. They wedge in perfectly to the space now. The EQ units are parametric, which means the center frequency of each of the 5 filters is adjustable. A paragraphic EQ is more typical, where each control covers 1/2 or more octaves, but it would take a 31 channel paragraphic to do what this 5 channel parametric can do for me in this situation.
5) Once I get the EQ units installed and any bugs worked out, I will take the sweep generator, a good microphone, and FFT software to adjust the frequency response of the entire system; HU, speakers, amps, sub, and the acoustics of the vehicle. I know most people will not go this far, but I just thought I'd share all this.
The reason I need such good sound in my car is that my wife cannot tolerate the volume I like to play music at in the house on my electrostats. Now I just rattle the spare tire and it bothers nobody, with the added benefit that my wife rarely rides in my car anymore.