Tokyo has a great subway system (for the most part--there are locations that aren't that well served) and there's good train service between many moderate-sized cities in Japan. But my experience is that, once you get to a city outside of Tokyo, the public transportation options aren't great.
Not really a bad experience but I was able to walk as a tourist to where I wanted to go because the areas were pretty centrally located. The one time I took a bus to somewhere--don't remember location--it wasn't that convenient.
Kyoto has a lot of buses, so maybe that’s where it was. I’ve found that they’re usually on time and not too crowded, but maybe you had a different experience.
