We did Japan in March 2023 as part of a bigger Asia loop that also took us through Taiwan and South Korea. Tokyo was the anchor — we stayed four nights at the Tokyo EDITION, which put us within walking distance of the Tokyo Tower and a short Uber from everything else.
For activities in Tokyo, we did a 1.5-hour Shibuya walking tour through to get oriented at the crossing and Center Gai, a Tsukiji outer market food tour the next morning, and a Shinjuku tour later that same afternoon. The one don't-miss we'd push everyone toward is teamLab Planets in Toyosu — it's the immersive digital art installation where you wade through water and walk through mirrored infinity rooms. Plan a midday slot and book in advance. For food, the conveyor-belt sushi at Sushiro is great cheap fun, and Gonpachi (the Kill Bill inspiration) is worth the walk for the atmosphere alone.
We then took the Shinkansen from Tokyo to Shin-Osaka — get a bento and a window seat on the right side and you'll catch Mt. Fuji about an hour in. In Osaka we stayed at the Courtyard Osaka Honmachi for four nights, which we used as a base to day-trip into Kyoto and out to the Yoshino-Kansai area for cherry blossoms (mid-March was a touch early but we caught the start of it). Osaka itself is a food city — Dotonbori for the giant crab sign and street snacks, Shinsaibashi for shopping, and the rooftop of the Umeda Sky Building for a view over the whole thing.
In Kyoto, we went to Fushimi Inari at opening for the red torii gates before the crowds, then over to Arashiyama for the bamboo grove and the monkey park, Kinkaku-ji (the Golden Pavilion), and Nishiki Market for lunch.
Japan is definitely one of those countries we would return to any time as a stopover or full trip. The food is delicious, the culture is unique, everything is peaceful and serene, and there is always just more to see.