>>42375031-54 Uenokoen, Taito City, Tokyo 110-0007, Japan
This spot has multiple outdoor floors. Get to the top and you can see the Ameyoko sign.
Mori Tower Roppongi has arguably the best view of Tokyo Tower. Go there at golden hour for the sunset and stay for blue hour.
In Kyoto, if you're able to rent a car, go down to Wazuka. 30 minutes south of Uji, it's got great biking opportunities and the tea fields make for excellent landscape photos.
Near the famous neon Dotonbori sign in Osaka, you can find buildings with external staircases. You can photograph the sign from above at a slight angle and it looks great.
Go down to the Gion area in Kyoto in the evening and maybe you can get some nice snapshots of geisha or maiko. Best spot is probably Hanamikoji-dori.
Kyoto is pretty empty at night, even during peak tourist season. I recommend checking out Yasaka Pagoda and Sannenzaka/Ninenzaka after dark.
Can't skip Miyajima island when you're in Hiroshima. I recommend biking around the back of the island if you're able to handle the steep hills. Nice beaches and shrines that aren't very crowded on the other side. Stay for sunset at the Great Torii if you can. Ferries back to Hiroshima run until like 10:00PM, just check the timetable, so you can stay pretty late.
This is all I can come up with off the top of my head. Good luck anon, let me know how it goes.
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