My top tip is, since everyone loves Fushimi Inari Shrine in Kyoto, there's actually a fantastic natural trail network there that I saw no one on. It takes you out through a valley of smaller shrines and graves, and nearly to the top of the mountain still. Then you can take the gates walk on the way down if you still want that experience. The trail had a beautiful uninterrupted view of Kyoto from a natural clearing in the forest canopy. Some of my best photos were from that little diversion.
When my wife and I went, I think we "accidentally" went on this trail. Our philosophy is to do the touristy things, but go just beyond what most do. This meant walking past the shrine and onto the trail network where we ran into a number of smaller shrines one the walking path.
Overall I was very impressed with the number of managed walking paths when we were in Japan. Allowed you to get away from the crowds pretty quickly if you'd like.
