Update July 8th, 2012.
Peace everybody, hope your audio projects are reaping many rewards.

In the ongoing exploration of the RTA process I was having great difficulty in achieving consistently good sound quality over a variety of the music I listen to.
I discovered a fundamental flaw in the method however. I was basically trying to tune over the Pioneer autoEQ results, which in effect is "un-tuning" the resulting Pioneer curve. So basically the Pioneer autotune creates this EQ curve (which looks like God knows what) and I was trying to use RTA and the 31-band graphic EQ on top of this. No wonder the sound was strained and artificial (for lack of a better term).

So in a fresh start, I turned the auto EQ off. Then I listened to the system completely flat for a week or so. While it did not sound spectacular, it did sound completely clean, easy to listen to and more importantly sounded like this for every CD I played. Gone was the strained processed sound and occasional harshness. I could also turn the volume up extremely loud and it would sound great. No longer did I have to reach for the EQ or crossover or network level controls on a harsh Mark Lanegan vocal, for example. Everything was CLEAN. This was promising, I thought. Needed a little work but promising.
After running flat for a week, I put the mic to the sound and did an RTA session. It showed a very high bass and mid bass region (plus 10-15db or so) and a few peaks in the midrange and lower treble regions.

I made a few EQ cuts in these areas, attacking the peaks with a moderate cut, then a smaller cut on either side of the peak so as to smooth the transition in the system from unit to amp to speakers.

I have lived with this for about 2-weeks or so and I must say it does sound very nice.

In an experiment I did switch the auto EQ back on a few times. The strained midrange / vocal sound returned immediately, although the bass did sound more punchy and dynamic.
I will soon do an RTA session to see what the bass region of the auto EQ looks like and see if I can duplicate it with a little EQ magic.