I also have been disappointed with some areas in Japan. For example, I visited Kamikochi Park in Japan. In the park they restrict entry to a limited number of taxis and tour buses. So, we are hiking along, nice view of the river, and we come around a bend, and there is a nice view of a bus parking lot (conveniently located next to the river)! That and the park decided to build two hotels right next to the river.

So the problem in Japan, is that they seem to do a poor job of balancing access with preserving the natural landscape. The same for many hiking trails, which often use concrete reinforcement rather than more natural materials.

As to numbers at national parks, I don't think the number of Japanese visiting national parks in Japan compares to the number of visitors in the US to national parks. For example, a smaller park in Maine, Acadia National Park, gets close to 7 million visitors a year. I can't imagine most of the national parks in Japan get anywhere close to that number of visitors.

http://www.env.go.jp/en/nature/nps/np.html

This link shows the number of visitors over 50 years (!). Some 390 visitors over 50 years, or about 8 million a year for all the national parks!