I can't help with things to keep a toddler occupied but for fall, my favorite area is Tohoku - the area north of Tokyo. Sendai, Matsushima, the mountains in the central part of the country. All will be ablaze in fall colors and the pace is slower and less frenetic than Tokyo or Osaka.

For a real trip out of the ordinary, consider Hokkaido. Hakodate is one of my favorite places to visit and Sapporo is one of the classics.

Matsushima in fall.



Hakodate morning market.



Kushiro harbor, Hokkaido.