When we were going to travel to Japan for the first time, we thought that we have to work with a travel agency. We thought that everything was going to be complicated, and actually, when we started to look for information, we saw that you just need a little patience and a lot of envy to read.
Japan is so organized that you do not need a travel agency for planning your trip, you just need to plan everything before departing, and write your own schedule, and all it’s going to be exactly like that in 99%.
Take into account my tips and you will be able to organize your own trip to Japan at your rhythm. In that way, you will probably find better accommodations at the same price proposed for an agency, or visit more cities, or spots you are interested in, and not only the tourist stops included in an organized journey.