Sony hasn't ever been at the top of my list, but that's mostly stubbornness on my part - I felt that they have often charged more than was warranted simply because of the "Sony" name. That being said, I do admit that the ES line has long held a very respectable position in the market, so I certainly wouldn't ever try to make a case against using a receiver like your old 3000ES - it's good stuff. Like you, I don't know much about the current generations of ES gear, but the older stuff at least has a good reputation. And Sony is certainly not alone in choosing to skip THX certification and stand on their own merits - it's the exact same thing Outlaw's done, and there are several other home theater separates manufacturers who fall into the same category.
That may be true, but you changed too many variables to be certain of that. I think the only real way to compare the 7125 to the Sony's internal amps would have been to connect the 7125 to the Sony and re-calibrate using a calibration disc (not internal test tones), then compare those values to those found with the 990/7125 combination using the same calibration disc. At the end of the day, I don't see any need to worry about it, as the important part is that the system is calibrated.