Going to Japan in July with my wife

So as the title says I'll be going to Japan in July for 3 weeks. We are visiting Osaka, Kyoto, Nara, and Tokyo. I have a decent list of things to do in each place, but if there are any really cool ones I'm missing let me know. We also need help on restaurant choice specifically those you need advance reservation to get into to. Only one I know of right now is the Pokemon Cafe. My wife and I enjoy shrines and nature stuff, anime and manga, and pretty much all things food and pop culture.

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Osaka (staying in the Chuo Ward at doutonbori crystal hotel)- get icoca card, Ichiran Ramen, aquarium, Shinsekai, Dotonburi, Shinsaibashi, Osaka Castle, Sumiyoshi Taisha Shrine, Umeda Station, Universal Studios Japan.

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Kyoto (staying in nagakyo ward near nijo castle)- Fushimi Inari Taisha Shrine, Kiyomizu-dera shrine, yasaka shrine, gion, food somewhere in pontocho, Arashiyama Park, Kinkaku-ji Temple, Maruyama Park, Nijo Castle, maybe day trip to Koka or something around Lake Biwa.

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Nara- Buddhist Temple, Nara Park, Kasuga Taisha Shrine, and I don't know what else.

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Tokyo (staying in shinjuku near Kabukicho)- Akihabara, Tokyo Skytree, Solamachi, Meiji Jingu Shrine, Shibuya, Hie Shrine, Asakusa, Senso-ji, pokemon centers, shinjuku, harajuku stuff, pokemon cafe, samurai museum, tokyo disney, Ueno Zoo, National Museum of nature and science (worth it?), imperial palace, robot restaurant?, tokyo tower, animal cafe (shiba inu maybe), ginza, tsukiji fish market, ikebukuro.

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Any suggestions or comments appreciated. Also typed this fairly fast so sorry for any typos or mistakes.