Itinerary might depend a bit on what time of year - do you have an idea yet?
How long will you have?
Definitely have a look online and think about what your interests are. Japan is amazingly varied, we love the contrast between the cities and the stunning mountain scenery.
We went to Tokyo and Kyoto, plus the Fuji Five Lakes region, travelled around the Japan Alps, down to Hiroshima and Miyajima and around Kyushu. Next time we’ll go to Hokkaido.
My favourite area was the Alps, so many pretty villages and amazing scenery. The Alps are accessible from Tokyo and Kyoto so doable if you have time and are set on Tokyo and Kyoto.
Hiroshima is very interesting and Miyajima beautiful. Not far from Kyoto so again doable for you.
Kyushu might be too much for this trip unless you have longer than a couple of weeks, if you can make it that far it’s lovely and different from Honshu.
Hokkaido and Okinawa would again be too much if you only have a couple of weeks but an option if you’re going for longer. Depending on what time of year you’re going.
General tips - stay in a Ryokan at least once. We love Ryokans and stayed in several and the whole experience is amazing.
Plan to try lots of food and do some research on where to eat as there are amazing options.
Plan a mix of city and countryside, as I mentioned it’s really diverse.
Try and get away from some of the busier spots in Kyoto. Kyoto’s most famous sites we found to be extremely busy with coach loads of tourists so we were glad to have day trips to places like Nara which, although busy, wasn’t as bad as other spots like Arashiyama.