I've read it twice now, and I think one of the things that Tim is unable to articulate is the Japanese inability to assert individual freedom. There's sort of a cargo cult mentality going on, where the Japanese salaryman (or his younger ronin counterpart) looks to tradition and/or media to shape his behavior, and strives for originality when all he's really doing is combining familiar things. That's not to say we're not guilty of it in the west (as any man who has dressed up as Magenta for a showing of Rocky Horror can observe) but we're more comfortable being offensively independent in our thoughts and actions. But Tim's reaction seems to be "Why can't they break out of this rut?" when the real question to ask is "Why are they so afraid?"
Based on the information Tim has collected all in one place, I see great fear in Japan. Boldness and valor exist only in fiction, which culturally speaking is the equivalent of peeking around the corner. Americans and Europeans boldly stride around the bend with bells on their toes and holding a banner aloft to flap in the wind. Sometimes, that first guy around the corner gets shot, but it's not long before a million more Yankees or Foreign Legionnaires or rampaging Vikings come thundering past the one fallen sacrifice. The Japanese, by contrast, see the one guy who got shot and immediately think "Shit, I don't want to be like him" and then just sit behind the wall, sneaking a glance every now and then and imitating whatever invention or fashion they happen to catch sight of.
I'm not sure if the otaku phenomenon outside of Japan has any influence on this insulated nature of the culture. You have these obsessed city-dwelling Americans who claim to love all things Japanese without any substantive understanding of the culture, and like a novice surgeon they reach in from outside to feel around and see if they can figure out what's making it tick. Are the Japanese able to grow and overcome their fear with all these hands figuratively reaching into their colon?