Animal-themed Tourism

My kids and I are learning Japanese, and planning to go to Japan after we finish the full course (we won't be anywhere near fluent, but should be able to understand directions and such). My daughter is super excited about all the animal-themed tourist spots in Japan. My son is a Nintendo and Gojira nerd – with a very low tolerance for crowds and noise. I am a medieval history/calligraphy enthusiast, and my husband is a foodie. Kanazawa appeals to me. Tokyo appeals to my daughter, but I'm concerned that it would be too crowded for my son to enjoy. I assumed Kyoto would be a happy medium, but I keep hearing how they don't like tourists. I am hoping to get some recommendations from people with a better knowledge base.

by ObviousAnony