One of my favorite things about Japan is the domestic travel.
The domestic JAL flights are the best I've ever experienced in my life, the train travel can't be beat, and even the infamous crowded subways aren't that bad.
Even though it's a bit expensive, taking the Bullet Train is one of my favorite ways to travel, and I'd rather spend the money on that than go via highway bus. It's a wonderful experience, and you can really see the country too!
I opted for the Puratto Kodama, which saves you about $45 and comes with a free drink from the concession cart and a reserved seat. I recommend it!
*The only draw back, if you miss your train you are out of luck, your reserved seat can't transfer to any other train.