Nara is well worth a day trip from Kyoto with the town and shrines easy walking made even easier hiring a bike near the station.
Nikko is well worth a day trip from Tokyo though the temple site is rather hilly.
Hiroshima and Miyajima Island to me are standouts though admit I am biaised.
My father was based in Hiroshima City for over four years as part of the British Commonwealth Occupation Force (BCOF). The US and Brits rather sensibly delegated care and control to the Australia forces with my father at one stage the senior allied member based at Hiroshima City despite being only a Flight Sergeant. Some may find some of his recollections of interest:
We reported to Richmond and boarded a DC3 (Dakota) for transport to Iwakuni. This was the regular courier flight and we went via Melbourne, Adelaide, Alice Springs, Darwin, Morotai, Samar (Phillipines), Laoag, Okinawa and finally Iwakuni.
Towards the end of 1949, a major fire swept through the squatter establishments in front of the railway station and the local authorities wanted to take advantage of the opportunity to implement their plan for the area. There was much argument about the plan, as the squatters claimed that it would destroy their domestic rights. The argument was finally resolved by Australian army engineers clearing the area with their bulldozers and making space for the start of the planned boulevarde across the city. I left before it was finished, but I believe that the boulevarde is a great asset to the city.
I must have pleased some people in Hiroshima, because when I left in early January 1950, I was presented with a ceramic bowl made from clay from the site of the atomic bomb and bearing the signature of the then mayor of Hiroshima.
Before departure from Japan, the RAAF wanted me to sign up for a further twelve years service which I declined. Some months after I left, the North Koreans invaded the South and once again the RAAF was at war. 77 Squadron, who had been packing up to depart the BCOF were the unit involved, with their Mustangs and later Meteors. In fact, a graduate of the language school who had returned to aircrew training was the pilot on duty when the invasion took place.