Buses are a little bit more difficult for me to use since most of the bus signs are written in Kanji (Chinese characters).
Since there are so many people in Tokyo, taking the train is a way of preventing congestion on roads. Just like carpooling, trains are able to transport a lot of people with fewer vehicles. In that way, trains are beneficial for the environment.
Trains usually stop around midnight and start up again around 5:00 a.m. Because of this, people either head home from parties or events around midnight or stay out all night until the first train. The train schedule and the few hours that the trains are not running often affect people's outings and how they plan their evening and morning trips.