WE will be in Japan for 3 weeks (March 8-28) and we are a family with a 6 year old girl. I already have the vouchers and now I am deciding what to see. This will be my husband and I's second time to Japan. We were there for 2 weeks 7 years ago, but will be returning to some of the same places.
So, arrival in Tokyo (5 nights there)
then take a bus or local train to the 5 Lakes area near Mt. Fuji. Stay overnight, then take a bus to Hakone area and stay 2 nights. I don't want to activate the J-rail pass just from Tokyo to Hakone which would be wasting days because its so close.
Hakone to Kyoto (3 nights)
We are planning to be in Onomichi for day 6 of the JRail pass then leave on day 7, but I am having trouble deciding on another destination after Kyoto before Onomichi. I have never been to the Sea of Japan area and am considering Kinosaki onsen or Kanazawa for one night, but from there we'd have to get to Onomichi, so it probably would be better to either make Kanazawa a day trip from Kyoto. Going from Kinosaki to Onomichi seems long with too many changes, so probably not a good idea logistically.
Maybe you have some other suggestions of another place to go overnight after Kyoto?