Visiting Japan for the first time can be confusing, try Okayama.
We went to Japan on our own for three weeks, in November 2015. We found two of the major cities very confusing and difficult to navigate. These were Tokyo and Kyoto.
We spent three nights in Tokyo and a week in Kyoto.
It was good to use Japan Rail. We had bought a Japan Rail Pass in the UK, which is necessary since you cannot buy it once in Japan. The JR Nozomi bullet train carried us smoothly from Kyoto to Okayama.
I recommend Okayama as a stay of about a week, because it is a small centre and much easier to find your way around. We stayed at the excellent Hotel Gran Via, which is in the station complex so a doddle to walk to, with your wheelie cases. The room was large and comfortable with a nice bathroom, alas not the case with our hotels in Tokyo and Kyoto.
From Okayama you can take day trips, using your rail pass. We went to the island of Shikoku which meant a fascinating trip across the Inland Sea on the famous bridge. From there you can take further trips to see more of Shikoku.
Another day we went by bus to the famous garden of Korakuen and admired the Okayama castle from across the river, though we did not visit it.
In addition, the last day we took the train and then the local bus to the delightful village of Tomonoura, which is preserved as a site of historical importance with its fishing boats and original wooden houses. There is no concrete new builds here, and we had a lovely snack in a hospitable cafe overlooking the harbour.