As you know, an airplane is the fastest vehicle in the world and it is good for crossing sea. Japan is a vertically long nation. If you like to go to Hokkaido or Okinawa, airplane is the best choice. The fare is not so expensive, which might be lower in off-season than that of Shinkansen. There are several airlines in Japan, two of which are famous for good service, JAL and ANA. But, if you like to reduce cost of transportation, you can make use of LCC, Low Cost Carrier, such as Peach and Vanilla Air. For example, it costs just about 5000 yen to go to Osaka from Tokyo in off-season or if you reserve the ticket early.
The disadvantage of using an airplane is the long distance between an airport and the central part of the city. For example, if you get off at Narita Airport, it will take about an hour or more to get to Tokyo station. Because you have to take a train or bus, you have to pay additional money, which is between about 1500 yen and 3000 yen, depending on which transportation you use.
If you visit somewhere which is not so far (say, Nagoya from Tokyo), you can use a Train or a Shinkansen, a rapid train whose maximum speed is about 300km per hour. Trains in Japan come to every station on time. Also, Ekiben, a lunch box containing local foods, is available at each station. Basically, the station Shinkansen stop is in the central of the city.
If your visa status is “Temporary Visitor”, you can buy Japan Rail Pass which covers all JR rails all over Japan which including Shinkansen. It costs about 10,000 yen for an one-way ticket for Shinkansen on the average. But, this pass is just 29,110 yen, and the term of validity is seven days. So, using Shinkansen, you can visit one city in one day, another city in another day without additional cost.
I don’t see so many disadvantages of a train and Shinkansen. But, Shinkansen is crowded with people in high-season so that you can’t have a seat and may have to keep standing for a few hours.
The fare is the cheapest among three public transportations. It costs about 5,000 yen. There is a recess every two hours. A bus stops at parking area which has a kind of a small mall. You can buy some snacks and drinks, also some local souvenirs are available. Some buses have a toilet, and reclining chairs are comfortable enough to take a nap.
It takes a lot of time to arrive at your destination. For example, it takes more than eight hours to go to Osaka from Tokyo. Some buses doesn’t have English announcement, and there is no staff who can speak English. You may have no idea where you are right now.
If you have a plenty of time, you can take a ferry from Osaka to Okinawa. It takes two days, but you can enjoy watching sea. Also if your visa allows you to do, by ferry you can go to another foreign country. You can go to Pusan, Korea from Fukuoka, and can go to Sakhain island, Russia form Wakkanai. Or, you can ride a bicycle for traveling. There are even some kids who traveled from Kyushu Island to Hokkaido by bike in the summer vacation.