One thing that's strange to me, having been all over the country myself (including Hokkaido, Shikoku, and Okinawa) and living in Aichi for a year, is that I only saw a wild small mammal once. Even that one time, I wasn't sure if I actually saw it, because it vanished before I got a good glimpse of it. I know there are squirrels somewhere- there's a native word for squirrel- but I've never seen them. Being from the northeast US, the concept that a location with a temperate climate lacking in abundant squirrels could exist seemed absurd. On my next trip to Japan, I will dedicate some portion to seeking out native squirrels.
Of course in Japan there are also a few places known for wild monkeys that like to hang out hot springs, but I haven't seen them in person either.
I did see a guy with his girlfriend hanging out on a mountain pass in a wrecked "panda trueno" that was being loaded on a flatbed when I was hiking once. I hadn't brought my real camera that day, and I deeply regretted it since my flip phone only had a VGA camera.