It seems there are two types of gca critics - the free flow (left brained?) and the right brained, measure it somehow type. For the free flowers, I doubt any sort of detailed explanation, system, etc. would seem acceptable, since they "know it when the see it."
Just like writing down any good thought about design that we generally follow - like bigger greens for longer shots - the minute it is written down, it becomes cast in stone and seems somehow less desireable. I think the same sort of holds true for the hole by hole analysis - its done so often its easy to get tired of it, see its faults, etc.
However, as Mike N points out, people have probably been analyzing course design since the week the Old Course opened and any time you attempt it, you must organize your thoughts somehow. Hole by hole is as logical a place to start as any, and there are flow charts, wind charts, shot sequence charts, green angle charts, fw width charts, green shape charts, uphill-downhill charts, etc. to finish the job if a simple hole by hole analysis doesn't seem enough.
I guess the question to Adam is, what system would you propose as an alternate? Why would it be better?