FWIW, Osaka is way worse than Tokyo. And of course nothing I said disagrees with your statement that the Japanese are not hard to get along with: of course not, as soon as you have established some sort of relationship where each person can place the other in hierarchy and responsibility, there are clear rules on how each will treat each other. And since the Japanese are really good at following rules, there won't be many problems. I think it would be better if they just replaced all the silly class/status/relationship based rules with one overall rule that says "treat everyone well," but...
You make a good point that the countryside is going to be different than the big cities, as people are less rushed. But overall, the cultural problem with not acknowledging the existence or "rights" of strangers is pervasive everywhere I've ever been in Japan.