Train is the most convenient and fastest way to travel around Japan. So it is worth buying a Japan Rail (JR) Pass.
We bought our pass online and received our voucher before we travelled. On arrival, we have to exchange the voucher with a pass. Unfortunately the pass only allowed us to travel within city without a ticket (had to show the pass to the guard to get entry and exit). To travel long distance, we had to queue at the travel office to get a ticket and reserve our seats.
I have to say it didn’t take up too much time, but you do have to planned ahead. As we were there during the typhoon season, our travel was delayed for a few hours in Kyoto but we still managed to change our tickets to get onto the next available train back to Tokyo.
The bullet train (Shinkansen) was really impressive and almost always on time! It’s very clean and the train station always have lots of food stores. That allow us to always buy snacks and not to mention the amount of vending machine that sells drinks.
You can also catch amazing views of Mt. Fuji while riding the Shinkansen from Tokyo to Kyoto, which goes up to 200 mph, into town.