Hi all, I have 16 nights in Japan in January. I have 2 kids aged 3 and 7. I’ve been to Japan 3 times but never with kids or in winter. Therefore we are not going to a few places we have already been multiple times.

Any suggestions or concerns with this proposed itinerary?

Tokyo - 5 days
Takasaki - 1 nights (en route to Nagano)
Nagano - 4 nights (including day trips)
Nagoya - 3 nights
Hakone - 3 nights

fly out of Tokyo

Can't really speak to the itinerary as I'm not sure what your wants are in those places, but I wondered if a trip south to Okinawa might be nice for the kids. It'll be in the 60's, so a visit to the Aquarium might be nice for them, and time in Naha along Kokusai Street. Lots of family friendly foods like coco ichiban curry, or Blue Seal ice cream and Mos Burger/A&W. Sumanume in Naha has the best Okinawa soba. Cherry blossom festivals start there in Jan-Feb, and you might be able to go on a whale watching tour. May be a nice break from the cold. Good luck planning!
https://visitokinawajapan.com/

Also, wanted to mention this California woman's travel blog. She's mainly a recipe site, but posts about travels with her young children, too. Maybe there'll be some tips there: https://www.justonecookbook.com/tags/chubu/

Thank you I’ve always wanted to go to Okinawa so I’ll take a look. We are actually traveling from Australia in search of respite from the heat!

Oh, of course! Yes, those mainland-Japan temps should be welcome.

If you find you are interested in Okinawa, I know many stay up north near Motobu for nature/beaches/the aquarium. My brother and his family stayed in a lovely airbnb by the aquarium. We've also stayed in Chatan near American Village at the Lapin Mihama hotel. I only recommend this location if you have a rental car, though American village is walkable. Sort of a midway point between Naha and the north of the island.

But in Naha, we stayed in a rental for a week, then just for a change, we moved to Tokyu Stay Naha in a residential family room, which was very comfortable. Close to the monorail, but I also found it walkable to Ryubo/Palette Kumoji (the start of Kokusai Street; also the central bus terminal). Onoyama park is just across the river (walkable), and may be nice for the kids.

Have fun planning!