I have a lot of experience with escorted tours in many different places around the world, and JTB tours are for you if you're accustomed to the "Asian style" of touring. The pace is very quick (as usual with most tours run by and especially for Asians), so if you are the type who need a lot of leisure time at each place, you will find it frustrating. However, this type of tour is a very good introduction to visit areas that you may want not be able to get to efficiently on your own.
We did the 4-day highlight tour that went to Mt Fuji, Hakone, Nara and Kyoto, round-trip from Tokyo. The last day of the tour was one free day in Kyoto, which we were very well prepared for after a full-day Kyoto tour the day prior--it gave us ideas on where to go that the tour didn't have a chance to visit. We had a very pleasant experience overall and were able to see everything efficiently. While I did wish we had more time in some place, you can't have everything! I would avoid signing up for tours that take you shopping, because you simply will not have enough time. Also, read the itinerary carefully before you sign up. Many of the combination tours have days that are really half days only, and it might not be worth your money. Try to pick tours that have a full schedule for each day. The itineraries are amazingly accurate to what you will actually be seeing and doing.
Overall, JTB is very very efficient. Their efficiency and way of operation is impressive. They put their resources at the point of use, so each person is only responsible for a small chunk (i.e. one person to gather people at check in, one person to bring the guests from the train station to the hotel etc.) and they are extremely organized! Because they piece together many tour groups together in different combinations, the people you are travelling with are all on a different itinerary, so there is no set group or tour guide that you will be with for the entire duration of your trip. If you're on a multi-day tour, you will see different people come and go everyday. We actually saw some people that were on our tour the first day again later in the trip. Therefore, if you are travelling alone and hoping to meet travel mates, you will most likely not be able to build that relationship.
The tour guides are good for the most part, especially this one lady who was originally from Osaka that took us to Mount Fuji. They provide very interesting information, are very well organized and are friendly. The only thing is that you cannot expect their English to be perfect. Most of them do have thick accents (which personally I found somewhat difficult to understand), but they are otherwise fluent for the most part.
Transfers were very well organized. We had absolutely no problems being taken to and from train and bus stations. The luggage transfer assistance was also very good--no problems both ways.
Lastly, if you're in Tokyo, I would recommend not doing tours that are within Tokyo itself. You can probably travel the city much better on your own as the metro is superb. But trips going outside of Tokyo are worth it!
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