Is this your first trip to Japan? How much do you want to spend on a ryokan, keeping in mind that it typically includes half board? You may also be able to book a night without dinner or meals which might be a good idea for a 3 night stay if it is in an urban area as the set dinner menu usually doesn't vary a lot each night.
Hakone is a popular stop for onsen ryokan between Tokyo and Osaka. There's also the less direct Hokuriku shinkansen that starts from Kanazawa which is a more traditional town, slightly less tourists than Kyoto, and good seafood. You can reach Shirakawa-go from Kanazawa by bus.
Japan has convenient luggage delivery services which typically take 1 day within Honshu and 2 days to the airport or Hokkaido/Okinawa. If you send your luggage from Tokyo on the morning of night 5, it will be waiting for you in the hotel room when you arrive at Hilton Osaka. The Hilton Tokyo is able to help send luggage from the Front/Concierge desk. You could also forward a piece of luggage from Osaka to NRT and combine into a single bag (or two smaller bags). It can be tedious to take two checkin size suitcases between cities yourself as there isn't a lot of room on the trains for anything larger than a carry-on and train stations are stair-centric.
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