As I was reading the comments about the obasans, I was reminded that I have been dealing with this behavior every morning on the train platform. Except its not an obasan..... it is from two 40-50 yr old American men in Texas. Rude, inconsiderate and overbearing is a learned behavior and not limited to cultures.
Natto - well Tsuawuki its seems there is about half of Japan that agrees with you .... and the other half with me.
The apology issue is not a problem for me. I was raised by someone who always expected forst the apology and then details to verify I knew what my mistake was. I prefer the briefer Asian assumption that the reason is known, though I tend to lapse into what I learned growoing up.
The segration in schools is nothing new to me. From at least 6th grade on, my U.S. public schools all segregated the PE classes and sport (that was 6 different shools in three different parts of the country, so it was a good sampling.) Unless it was homemaking or shop, it didn't usually happen in the classroom - at least not formally.
The only thing I would expect to have problems with (when I finally get to visit) is the smoking.