Well, it's much more rigidly structured and formal than anything you normally see in the US these days. Plus, you tend to exacerbate things when you give them "exotic" titles, and you get people here who are more Japanese than Japanese people in Japan.
The question is - why add an additional cultural layer, and what does it really get you?
It certainly is more structured and formal. And that is exactly what I like about it. The down side is that just like a few decades ago in Europe things can become too rigid. It is however not as I experienced it, quite the opposite; a relaxed atmosphere seems to come naturally with a certain amount of formality.
You have stayed quite some time in Japan. Did you feel the formality and social structure as a constant hindrance?
Your second point is true enough and I have seen plenty of examples of this - but is this not also a matter of education and experience? It is a bit like thinking that every Dutchman wears wooden clogs (I do actually, but that is beside the point). Once someone has been in the Netherlands he knows better.
Your last point is of course an open question. It is up to each individual to answer this for him/herself.