Getting Around Japan: Planes vs. Bullet Trains
If you're visiting Japan from overseas, a ride on the shinkansen might seem mandatory. In many cases, visitors who land in Tokyo and wish to go to another city might find the bullet train to be the best option. It's also a relatively economical option if you plan on getting the JR Pass, which includes free transit on all JR trains. However, if you're going to Hokkaido, Shikoku or Kyushu, flying may be the better option. There's a lot to consider, so weigh your options carefully to avoid wasting time and money.
The single most important factor for car-less tourists is usually convenience. If you're traveling from city center to city center, the shinkansen is almost always going to beat flying. Shinkansen stations are usually centrally located, often at the major hub for all other local train lines. Tokyo's Shinagawa Station is a short ride from Shinjuku and other major destinations, and the Tokyo Station terminus can be accessed via 8 different local train lines.
On the other hand, Tokyo's Narita Airport is a 50-minute express train ride outside of the city center, and Haneda Airport requires at least one train transfer for many passengers to get to. There's also the hassle of dealing with security and checking baggage at the airport. Unless you're heading to another city directly after landing in Tokyo, the shinkansen will usually be more convenient than flying.
Believe it or not, flying can often be cheaper than the shinkansen! If you're heading to a far-off city like Sapporo or Fukuoka, you may be able to snag cheap tickets from one of the Tokyo airports. Even Nagoya and Osaka airports sometimes offer discount tickets to various regional airports. These are worth looking into, especially if your hotel is close to the airport in one or more of your destinations.
However, individuals entering the country on a tourist visa are eligible for the Japan Rail Pass - which includes the shinkansen! Though the pass is expensive, it will probably pay for itself if you use the shinkansen to change cities at least once a week during your trip. Do some comparison pricing to see if you can save some money this way. (If you're entering Japan on a work or student visa, you're unfortunately not eligible to buy the JR Pass.)
Comfort and Ease of Use
Taking the bullet train is almost guaranteed to be more comfortable than flying. There's no turbulence, and it's easy to get up and walk around when you need to. There's also more legroom, typically. Though there's no free drink or meal service, you can buy bento boxes, soft drinks, beer, and other goodies from a stewardess.
Flying, however, can be much easier to use for people flying with large amounts of luggage. Though airlines typically charge extra for excess baggage, it may be easier to deal with that the minimal luggage space on the shinkansen. Shinkansen staff are generally not around to help you put your suitcase into the overhead racks on the train, and you'll annoy other passengers if you try to leave your suitcase in the aisle or in front of another seat!
Airlines vary in how and when they allow people to make changes to their itinerary, and alterations get even messier during peak tourist season when many flights are booked. The shinkansen is always going to allow you more flexibility than flying. In addition to having dozens of trains available per day, you can change your reserved ticket once with no additional charges, as long as the train hasn't left yet.
In fact, there are so many non-reserved seats on most trains that many locals don't bother getting a reservation! Reservations are highly recommended during peak tourist season, though, or if you're traveling more than an hour on the train. It's not a big deal to stand on the train for a half-hour or so, but you'll definitely want seats if you're going out to Hiroshima or Aomori.
Traveling with Bikes
Unlike many other countries, you generally can't bring assembled bikes on trains in Japan - including the shinkansen! Bikes that are broken apart and stored in a bag are generally fine to bring on either planes or the shinkansen, though luggage fees or storage space can be an issue. Consider renting a bike at your destination instead.
Reaching Small Towns
If you're going biking in Onomichi or heading to Morioka for a countryside retreat, flying to the nearest airport and then taking the local train would be a pain. Both of these smaller cities have shinkansen stops, though! While not every train stops at less-populated stations, you can generally expect several trains a day at every station. You also have the option of taking the shinkansen to the nearest major station, then taking the local train for a more scenic route.
Kyushu, Shikoku and Hokkaido
If your destination is outside of Japan's main island of Honshu, flying may be your best option. While the Kyushu shinkansen gets you to destinations like Fukuoka and Kagoshima, it doesn't go to Nagasaki or Oita (though a Nagasaki extension is under construction.) It also takes nearly six hours to get from Tokyo to Fukuoka by shinkansen, compared with just two hours to fly. Plus, Fukuoka's airport is one of the closest to its city center in the country!
Similarly, Hokkaido's shinkansen doesn't reach most of the island, and the Sapporo extension is still under construction. Shikoku doesn't even have a shinkansen route! Its express train connects with the shinkansen at Okayama Station, but it's inconvenient and should be avoided unless you're heading to a small town far from one of Shikoku's four regional airports.
While Japanese airlines are certainly more reliable and timely than many Western ones, they sometimes have to deal with bad weather and other problems. Even mild thunderstorms can cause ground stops and other delays. Flying in the summer can be quite the adventure, especially if you are attempting to make an international connection in Tokyo.
The shinkansen also has to deal with power outages, flooding, typhoons, and even earthquakes. In case of an earthquake, the shinkansen may be shut down for hours while the tracks are inspected. However, the shinkansen is still generally more reliable than flying. Also, since so many trains run every day, it's easy to get to your destination once service is restored
Dealing with Major Delays
Even if shinkansen service is delayed or suspended, local lines may still be running regular JR local or express trains. If service is suspended for an indefinite amount of time, consider taking a JR train instead. You may be able to exchange your shinkansen tickets and get a partial refund. The same goes with major flight delays - switching to the train may be a much faster option.