Just had 3 weeks in Jpn for rugby world cup, so our itin was dictated by weekend games/venues, then finding our way elsewhere thru the weekdays.
I lived/worked in Tokyo in the 80's, and the difference then and now was staggering. So so much more complicated and busy for any form of public transport, Tokyo in particular. Places I remembered (used to catch Ginza line subway from Shibuya every day) were unrecognizable, so make sure you know your route/subway line/exit gate etc, and save yr directions to phone when moving around Tokyo.
Kyoto, however was a revelation - beautiful temples incl Inari, Philosopher's walk, Nishiki food market is a Must, streets around Kawaramachi, make yr restaurant booking in the morning for places like Itoh Dining, but probly stay near the station because that makes subway and shinkansen easier. Daiichi Royal Grande was quite new, smart, adjacent to station and well priced.
One week, in-between games, we went to the Art Islands - adjacent to Okayama - easy short ferry trips between 3-4 islands all with fantastically modern art galleries - look up Naoshima and Teshima Isls, or go here :
benesse-artsite.jp
Wish we stayed onite at Kanazawa after doing the Alpine Route (not encouraged in Jan I wud think..) and wish it wasnt a public holiday our last night in town when Tonki's Meguro had a queue out the door.. An old fave tonkatsu place
Last night in Tokyo at the Station Hotel - if you want to completely relax and waft out of town then this is the place to stay.. Bellhop will walk you down to the Narita Express platform.