Highlights for me and the rest of the family (DC 24 & 26) we’re definitely Hiroshima, seeing the A dome was quite sobering and the museum and peace park were very interesting, we had a day on Miyajima which we all enjoyed too although it poured with rain and was very busy.
We found getting around using the Shinkansen was easy and very comfortable, other modes of transport were fantastic too. Trains run on time and there are usually plenty of them. We used buses quite a lot in Kyoto, just make sure you have plenty of coins. We had a special “bus coin purse”!
For views of the Shibuya crossing, go to the Magnet building, you have to buy a drink to go up but the view of the crossing was much better than Shibuya Sky, although we were there at sunset (take an extra layer - it got cold!) so a great view of Tokyo with the sun going down.
We had a tea ceremony in Kyoto, the lady that did the ceremony was so graceful and explained all the movements - so different to making a mug of Tetleys at home.
Nara is worth a visit, we had a morning there to see the deer and the temple with the huge Buddha that was shown on Race Across the World.
We also spent a day at Universal for my sons birthday which was great fun.
Im not sure if it is still available but Jane Macdonald did a series on Japan which gave us a few ideas (think it was channel 5).
I could ramble on for ages about how clean (no litter anywhere - take a small rubbish bag with you and hand wipes, some of the toilets had no hand drying facilities) and how respectful and polite everyone was, it was sometimes just the little things, umbrella bags so you don’t drip in the shops or you leave your brolly in the racks and it WILL still be there when you go back for it! 7/11 Lawson etc are great for snacks/ lunch. Edamame crisps were a particular favourite!
Take an empty suitcase because you will fill it with souvenirs and weird flavour kitkats!