You can read 1,000 lists that always take you to the same places. But this list will most certainly slant different.
I'm usually reluctant to make recommendations to people because I think it skews expectations. I believe expectations greatly affect happiness. Every experience can only be subjectively rated. I don't know what you generally like and don't like. Some of my favorite experiences around the globe are probably the result of good weather combined with good coffee combined with a good night sleep combined with a lack of tourists.
So keep this all in mind. Without further ado....
Shrines and Temples (Adult list)
Futagoji
Nikkō Tōshogū
Rin’nōji Taiyū-in (Mausoleum of Iemitsu)
Kotoku-in
Otagi Nenbutsuji Temple
Kiyomizu-dera
Shrines and Temples (Child list)
Nyoirinji Temple (Frog temple)
Fushimi Inari Taisha (Red gate shrine)
Go-ō-jinja Shrine (Boar temple)
Myouryuji (Ninja temple)
Sugawara-in Tenmangu (Ox shrine)
Amusement Parks (Adult list)
DisneySea
Edo Wonderland
Universal Studios
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Studio Ghibli (ugh)
Amusement Parks (Child list)
Universal Studios
DisneySea
Studio Ghibli
Edo Wonderland
Experiences
teamLab Borderless
Ferry from Osaka to Beppu
Ninja Cafe (Takayama)
Komodo rental
Origami museum
Yanagawa canals
Hakata doll painting
Porcupine cafe
Snow monkey viewing
Nara deer park
Tea ceremony
Go check out my guide for the best free things to do as well as itineraries and travel tips to make your trip unforgettable.