If you want to work out how much is walkable, you can put your destinations in to google maps and get a good idea.
For three days in Tokyo you can do: - one day exploring Shinjuku, Harajuku, Shibuya (sights include Meiji Shrine, Shibuya crossing, museums, etc) - one day exploring Asakusa, Ueno(sights include Sensoji temple, Kappabashi dori, Ameyokocho, Ueno Zoo, museums) - another day doing other areas like Akihabara, Odaiba or Ikebukuro or one of the many other areas to explore.
Three days in Kyoto you can do: - one day in Higashiyama area (Sanjusangendo, Kiyomizudera, Kodaiji, Yasaka Shrine, Gion, further up to the northern part if you wish/have more time) , and Fushimi Inari. - one day in Arashiyama (bamboo grove, Tenryuji, Gioji, Adashino Nenbutsuji, Otagi Nenbutsuji, Monkey Park, scenic train or boat rides if you wish) - one day exploring Nishiki Market and Nijo castle in the morning, and Kinkakuji, Ryoanji, etc in the afternoon.
Three days in Osaka you can do: - one day exploring Osaka castle, any temples/shrines of interest, Namba area - one day of Umeda area and Osaka Aquarium - either USJ or a day trip to Nara, Himeji or Kobe.
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