I agree with PWWeber. My wife and I visited Tokyo, Kyoto, Nagoya, Takayama, and Shirakawa-go over a 2-week span and had no "hassle" or "worry" about travel arrangements or luggage. Of course, we do travel light--just one carryon size suitcase each and a small daypack for medicines and such. In the cities we visited, public transport info is in several languages--always Japanese and English, usually Chinese and Korean as well. Depending on the city, we also saw French and Spanish here and there. You would have to be extreme worrywarts or inept to not be able to handle it pretty easily.
BUT it is your money and time, so do what makes you comfortable. I'm just letting you know that there is nothing to be concerned about if you are fairly intelligent people who don't get flustered about a minor mis-step that might happen along the way.
NOTE: Just in case someone misinterprets what I said about worrywarts and the inept--I'm not saying that everyone who takes a tour is an extreme worrywart or inept. Some people just don't like planning and studying before they travel. But anyone who isn't an extreme worrywart or inept shouldn't choose a tour just because they think traveling by public transport or handling luggage in Japan is a challange.