I think your approach ultimately is only useful for each individual on his or her own, to come up with his or her own "personal reference point." I don't think there could ever be a generally accepted sense of "neutrality," even as you have refined it with the different types of colorations.
I'd like to point out that the title of this thread is "How do YOU judge YOUR SYSTEM'S neutrality?" [Emphasis mine.] It is not, "I'm going to compel you to make your system conform to my idea of neutrality." It seems an obvious point, but it appears to have been lost in much of the discussion throughout this thread.
Likewise, Bryon, I think that although it may be possible to come up with a very lengthy list of different categories of colorations that many audiophiles could agree upon IN THEORY, I doubt that there would ever be much consensus on this IN PRACTICE, the result being that very few audiophiles would end up coming up with the same sense of "neutrality."
I disagree. My own experience with my system leads me to believe that if you could A/B the various types of coloration in an otherwise constant system, almost all audiophiles would prefer the more neutral system. Maybe Dgarretson or Almarg could tell us if such a test is possible on some of the forms of coloration (for instance, is there a way you could introduce and remove intermodulation distortion, harmonic distortion, crosstalk, etc.?), but how many audiophiles are going to prefer a boomy speaker cabinet, room modes, comb filtering, etc.? I had the opportunity to listen to reduced jitter in my system in two stages (first my adding a Monarchy box between my computer and DAC, then going with a DAC with asynchronous USB), and with each improvement, there we significant improvements in sound quality that I can't imagine any audiophile not preferring. I liked my sound before, but after reducing this form of coloration, I can not imagine going back.
I think personal preference plays its strongest role when tradeoffs are required. For instance, if one has to choose between an excess of speaker cabinet resonance, or having poorer resolution, it is likely that audiophiles would be split. But the choice between more or less cabinet resonance is simple, and I think most audiophiles would choose less.