Japan has one of the excellent public transportation in the world. If you are coming to Tokyo or Osaka, they are well connected with multiple train lines.
Going around by Taxi is expensive.
Moreover you can depend on Train in Japan. They are always on dot. Never late - unless there is some human accident and rarely during snow season.
If you are traveling by Subway or Metro trains, you get free WiFi and air conditioned with cold air during summer and warm air during winter. All the more reasons to go by train.
Bus is also on time in Japan. Rarely there is a need to use a Bus.
People maintain silence in train or bus how much crowd it may be. You have to maintain some manners while travelling by Train or Bus.
Train and Bus are convenient
+ Anywhere you go around in Tokyo (almost all places in Japan), you can go by train (or sometimes in bus)
+ Know your train route - JR or Subway or Metro
+ There are English route maps available almost in all stations in Tokyo and major cities and tourist spots
Maintain Silence inside train or bus
+ Avoid talking inside train over phone
+ Avoid talking or talking loudly with your friends
+ If you are wearing a backpack, remove and keep it in your hands
+ If you are listening to music with headphones, ensure the sound is not too loud that it may disturb others
Sitting in train/bus
+ Do not sit in "Priority seats"
+ Do not sit occupying two seats
+ Give your seat if any old person, pregnant ladies, women with baby or person with injury comes in front of you
+ There are manner posters everywhere
+ Follow them or just follow what fellow passengers are doing