First time visitors 14-16 day itinerary

My husband and I and 3 teenagers aged 18, 16 & 14 are coming to Japan for the first time on December 28 for up to 16 days.
Rough itinerary: ( 4 days Tokyo ) 2 days Tokyo city, plus 2 day trips to Nikkō and Fuji Five Lakes ( or Hakone? )
2 Days Hiroshima & Miyajima ( Ryokan stay ).
Kyoto via Himeji. ( 4 days Kyoto ) 2 Full days Kyoto + 2 day trips - to Nara & Osaka.

From Kyoto Via Kanazawa to Takayama and Shirakawa-go then back to Tokyo - this is the main bit I need help with. Where to overnight and how many days required? Recommended Onsen in this area for a stay?

Am also considering Okinawa and Yaeyama Islands in place of the Japan Alps region mentioned above - thoughts?

We would like to see a real mix of what Japan has to offer including Culture old and new, not just Shrines and Temples. Not big on shopping. Love food experiences. Love natural beauty. Enjoy walks.

Any suggestions appreciated.

Hi.

I would drop 2 Kyoto nights and stay in Nara for those nights. Heaps prettier, much more nature, less people, more deers. Brilliant for an early walk in the (massive) park and forest before the buses arrive.

Kyoto is nice enough in parts but is a very concretey city with the good stuff around the outside. The Kyoto station area is very drab though there are pockets of niceness. If you like nature, consider the Westin Miyako in Kyoto. It is a little out of the way of Kyoto Station but has great views and a walking track through a foresty hill. The Japanese rooms there are excellent and set in a nice garden area (no views), otherwise look for a room with views over Kyoto. Some of the other rooms are small and stuffy especially in winter when Japanese tend to think that there is no such thing as too warm.

For the Kyoto onward leg I would go Kyoto to Takayama (train, quite a long trip but very nice, recommend Hotel Associa there though it is a little out of town, very cheap for the quality) for maybe 2 nights then on to Shirakawa-go by bus for maybe 3 hours, then on to Kanazawa for 2 nights (Hotel Hakuchoro there is nice). Then you can go by shinkansen back toward Tokyo, and I would stop off at Karuizawa which is a pretty resorty town with some decent things to see and fun shopping. I'd stay a night (recommend Le Grand Kyu - great value and very classy, though Tsuruya Ryokan is also a great choice and in a nice part of town, it would be my pick for first time ryokan stays). There is a walk from the top of town to a temple and lookout that is part of the Nakasendo way, it is worth it and I preferred it to the Tsumago/Magome walk.

It is winter. You will encounter snow. Be prepared.

New years is very busy. Plan you trips around this otherwise you'll be standing for you long distance trips on trains.

I love Okinawa (particularly Kerama Islands) but I would totally skip it in December unless you want to do the mainland Okinawa and cultural sites.