90 Days in Japan with 2 Toddlers

We are planning to go to Japan for 3 months from mid-September to mid-December with our 2 kids (1.5 and 4.5 years old).

So far, our rough planning looks like this:

• Travel to Tokyo and stay there for 10 days.
• Move to Kyoto for 30 days and use it as our home base for day trips in the region (Nara, Lake Biwa, etc.).
• Fly from Osaka to Naha and stay on the Okinawa main island (probably in Onna) for 14 days.
• Fly to Fukuoka for about 5 days.
• Go to Hiroshima for 7 days.
• Go to Okayama or Kurashiki for another 7 days.
• 11 days TBD (any suggestions are welcome).
• 6 days in Tokyo before flying home.

As Japan has so many nice places it's really hard to choose an itinerary for 90 days, especially as we can't travel to so many different places because of our kids.

Any tips, suggestions, improvements? What would you change or do differently? Thank you!