The places recommended are all nice places. The situation you will be facing is that you will be visiting Japan during the foliage season. Foliage is mother nature, and it is difficult to predict when the peak of the foliage at certain locations will be this year. But anywhere with foliage will be very busy. If you want to avoid a busy cloud, then the key will be to avoid foliage.

Nikko is one of the top foliage destinations in Japan. You pretty much have to go through the main Nikko area to reach Oku-Nikko. Technically, there is a back entrance to Oku-Nikko without going through the main Nikko area. But from Tokyo that will detour you so much (and pretty much have to drive your own due to lack of public transportation) that from Tokyo you may end up spending more than half a day just getting to Oku-Nikko via the back entrance.

An example of how bad the traffic is at Nikko during the peak foliage season. From Tobu Nikko station to the entrance of the Toshogu temple, it is 1.5 km (0.9 miles) and it is usually a 4 min. local bus ride. During the peak foliage season, the Tobu bus is reporting 40-45 min. journey for this short 1.5 km (0.9 miles) due to the traffic. Going up the Iroha hill to Lake Chuzenji toward Oku-Nikko is the same situation. 16 km (9.9 miles) Iroha Hill is reporting 3 hrs. drive during the peak of foliage season. This is the annual event in the foliage at the Nikko area and the peak foliage season for the Nikko area is from mid-October to the end of November.

Another famous place with a foliage traffic jam is the Kiyomizu temple in Kyoto, which is famous for its Japanese maple trees. Usual 5-10 min. drive around Kiyomizu temple takes 40-50 min. drive due to the traffic. You may think it will be better to walk, but due to the number of tourists in the area, walking around Kiyomizu temple during the foliage season will make the morning rush hour at Shinjuku station look like a day at the beach.