Several rivers run through Tokyo and they are all polluted. Japan has a ways to go in cleaning up their environment.
I think we have been going through a bit of culture shock this time. It apparently happens to everyone but it has taken a little longer with us probably due to the short stays we have had here. After a while the way a different culture does things begins to grate a bit. Not that we aren't enjoying it this time, it is just that you begin to wonder about some of their ways and thinking. In Tokyo the sun sets at 7:00 so we miss the long evening you are experiencing now. However I don't think I would trade you weather for ours right now. It has been mostly in the low 20's since we have come.