It was meeeee! It was fabulous.

It is SO easy to get around. Everything is in English and Japanese. People are reluctant to speak English to you a great deal, but will listen if need be. The JR pass is a brilliant option (was for us, for 7 of our 20 days)
Accommodation-wise, we stayed in four places: a friend's house, a ski lodge type place, a hotel and a private room in a hostel. All were great. We got a good deal on all of them by booking online, but you can also book in-country.
We didn't go through anyone to book anything. Not really how we roll. We were given a Lonely Planet Japan, though, which was particularly good for finding vege-friendly restaurants.

You're in for an awesome trip! Good luck and have fun planning!