We took the Best of Japan tour and yes, it was packed and we were on the go. Thankfully, it was a small group of adults and we were all experienced and pretty relaxed. The "gardens" in Japan are often large parks because such expanses of parkland are considered rare and beautiful tourist areas for the Japanese.
I needed more free time to explore and finally realized that I would have to come back. Too often I wanted to say wait, what is this? and the group was a block down the street. My favorite memories are when we got to go alone and explore and talk to people (or try to). It is just the trade off to get the tour guide and the wonderful help with the whole transportation issue.
Steve: we had the funny experience of going into a restaurant and sitting down because there were menus and a waitress. Nothing happened. Watched when the next people came in and they went over to the "automatic machine" on the wall to place their order and pay and then sat down. We walked over to it and everything was in Japanese. So we waved the waitress over and she helped us while laughing at the foreigners. The whole place was run by the waitress and the cook and it was pretty large.
Another experience our group had several times was at the 7-11s where we changed our money at the ATMs. We would all buy things to change the large denomination notes and the cashiers kept giving us extra things. Finally found out they were having a contest of some kind and these were our winnings. One member got a bottle of wine.