On the cruise ship we stopped at three port cities of Japan, then we traveled over-land on trains to three cities, Tokyo, Kyoto and Hiroshima staying three nights each. Three days from the ship plus 9 days over-land gives us 12 days total in Japan.
Tokyo is really a large metro area with cities in it's boundary, our AIRBNB was in Shibuya, which is one of the cities in Tokyo. The first night we saw Godzilla's on top of a building and eat at a wonderful restaurant. We walked across "Shibuya Crossing" the largest crosswalk in the world! On a Friday night 3,000 people crisscross the road when the light turns green.
Kyoto is known for it's natural beauty and shines, however we found net Japanese things around each corner. Girls dressed as gil, and cherry trees starting to blomsem. The bullet train from Tokyo to Kyoto took about two hours with speeds reaching 100+ MPH.