Wayne,
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When all of the peaks are brought down (across the entire seating/listening area) the resonances are brought down with them, by default.
What about frequencies with long decay times that don't show up as peaks?
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In my mind though, that's doing only "half" the job. Although, realistically speaking, to do the "whole" job would require much more processing power (probably more than twice what it offers currently) and be absolutely prohibitively expensive, perhaps even for the very well heeled.
The Lex initially ships with 4 SHARC DSP engines. The room EQ feature adds 4 more. That still leaves room in the processor for 8 more SHARCs. Lack of processing power was not holding them back from doing the other "half" of the job. They are firmly against amplitude based correction. Keep in mind that if a peak is not associated with an unusually long decay time then it is left alone. It's not that they can't do something about it; it's that they deliberately don't do anything about it.
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Doesn't matter, as long as multiple microphones/microphone locations/samples are used in conjunction with spatial and temporal averaging, all of them will be detected and dealt with equally.
It matters, because it's the difference between guessing and knowing.

Again, how do you know which specific frequencies have the longest decay time? After correction, how do you verify that that actual decay times have been reduced? What are you using to measure decay time and generate corresponding waterfall plots?
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The shear number of samples taken from several different locations, averaged into a representative "room curve" of the entire listening/viewing area, will negate the effects you describe.
No they won't. Meridian, Lexicon, Audyssey and H/K wouldn't have resorted to using time-based measurements if amplitude based measurement would have allowed them deal with long decay times.
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If one can afford it, it would seem that Lexicon (Meridian, Audyssey and Harman/Kardan) EQ has a leg up on it's competition.
The H/K system is available on their AVR-435 receiver, which can be had for less than $500. The Audyssey system will soon be available on Denon's AVR-2807, which has a MSRP of $1099 (street prices will be lower). Not unaffordable.
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Sanjay