Tokyo (Skytree and general looking around, we also went to a baseball game), Hiroshima (there is an old building there still up from the bomb blast and memorials around which are nice), Kyoto (Watched a sumo wrestling tournament) and Miyajima (for the shrine), travelled around on the bullet train as there are good tickets for tourists, returned back in Tokyo and flew home. It is expensive but if you plan well (My family crammed it all in 2 weeks) and travel with rucksacks or not too much luggage, it is definitely worth it. The people there are very respectful, everyone you meet with will nod their head and treat you with utmost respect.
It's also completely fine and enjoyable to stay in Tokyo, there is a ton of stuff there that I haven't yet explored and I want to go again. Going up in the Skytree was very cool too!