We’re off to Japan in 2 weeks - very excited!
I’ve planned an itinerary to fit around DH’s work whilst he’s out there, and got some really good advice from Tripadvisor forums, but here’s what we’re doing:
Osaka - 1 night
Kyoto - 4 nights (one day tip to Nara in this time)
Hiroshima/Miyajama - 1 night (the 7 day JR pass will start the day we travel there
Kanazawa - 2 nights
Takayama (travel there by bus vis Shirakawa-go) - 2 nights
Hakone - 1 night in Ryokan with private onsen
Tokyo - 3 nights
I’m obviously no expert as I haven’t been there yet, but if you just want to focus on 2 places, I’d suggest basing yourself in Kyoto instead of Osaka (they’re really close if one of your flights is from Kansai), but depends what you’re interested in seeing.
There are literally hundreds of hotels in each place, so I just worked out which area of the town/city I wanted to stay by checking in my lonely planet book, and the searched for hotels with good reviews and in my budget. Nowhere fancy, and generally it looks like rooms in Japan tend to be very small, but we’re going to try and travel light so should be fine.
Enjoy planning your trip, and definitely try the Tripadvisor forums too as you’ll get some great tips there (from someone more knowledgeable than me I’m sure 