You should definitely not miss typical sightseeing places such as Kiyomizu Temple in Kyoto and Sensoji Temple in Tokyo.
Here is my opinion what to not miss:
Beautiful temples and shrines, historic architectures, Kyoto style Kaiseki cuisine
Lively atmosphere, Osaka food (Okonomiyaki and Takoyaki), Osaka Castle
Izakaya (Bar hopping), don't miss numerous and various places to eat and drink, shopping
Great nature and seafood and fresh vegetables, do something to enjoy Hokkaido's nature. Visit Biei to see the beautiful flower field. If you have a chance, hiking in Shiretoko's is extremely beautiful.