Hiking and historical sites are going to be the big focus of our trip as a whole. Gardens, shrines, UNESCO heritage sites, that sort of thing, and plenty of time outdoors. And we will most likely have 3 weeks (well, 23 days b/c weekends), including travel time, because that's about as long as I can possibly get away from work.
In Tokyo, my daughter wants to show us Asakusa and Akihabara, and we have to have a meal in Shinjuku because DD10 was fascinated by some of DD17's pictures of that area (and a rainbow grilled cheese) from this past summer. Beyond that, I'm not sure. I was thinking 4 days/3 nights in the city, but I'm not sure that will be enough or if I should add one more day. We're not shoppers as a rule and plan to travel light because we are going to be moving around so much, so I don't plan on a ton of shopping.
At Fuji Five Lakes, DD wants to hike Aokigahara to see the caves, and if the weather cooperates/the timing works out, we'd like to see the shibazakura festival at the base of the mountain. Hakone looks like it would be a decent "home base" for that and there is an onsen resort there that caught our eye, though I'm open to other suggestions for lodging in the area. Two nights in the area would probably make sense. We'll have a JR pass for the length of the trip but I'm planning on renting a car for these couple of days because it sounds like mass transit will be difficult for some of the places we're going.
I really haven't started digging too much into Kyoto sights we want to see, and DD didn't spend any time there on her trip so it'll be a first visit for all of us and I'm really flying blind on planning that bit. It is kind of the big blank spot right now on the itinerary, waiting for me to fill in some things. But that's why I've started researching over a year in advance!
There are also a couple of short stops I'm not quite sure how to work in. I'd like to see the gardens at Okayama, and DD17 wants to see Himeji Castle, but with so little familiarity with the train system and mass transit in general (I'm a lifelong Detroiter), I'm uncertain how to handle those stops that don't seem to demand a full day or overnight stay.
I think I'd like to stay overnight at Miyajima. DD found a hike there on a "best of Japan" list on some planning site, and the blogger spoke pretty highly of the experience of visiting the shrine outside of the hours when day guests are milling about. I don't anticipate doing much in Hiroshima except the Peace Dome and museum and going out for okonomiyaki, but my girls do also want to go to "bunny island" while we're in the area (they raise & show rabbits, so they think that's the coolest thing ever).
From there, where we go will depend on how much time we have left and what we decide to do with it. If we have the time, we'll either head south to explore Kyushu a bit (Nagasaki and Yakushima) before going back up the coast to Shimane to visit DD's host family, or we'll go straight on to Shimane and then travel up north toward the end of the trip (Kanazawa and Matsumoto at least, further if we have time). Or if we don't have time, we'll just do Shimane and then loop back to Tokyo.
The Shimane part of the journey will be planned for me by DD17 and by various members of the family she stayed with there - there's a silver mine that is a UNESCO World Heritage site that DD said we have to visit, and a shrine that is known as the home to the Shinto gods, and she wants us to hike/climb Sanbe-san (which she says is the easier of the two mountains she climbed when she was there), plus just visiting with her host family and friends. So the plan there is 4-5 nights.
At the end of the trip, I want to have 2 nights/3 park days at Tokyo Disney before flying home.