What transport passes do I need for this trip?

I am planning on going around 16 days to Japan in May-June. I want to go to the following cities in this period of time:
Tokyo
Kamakura
Hakone (on the way to Kyoto)
Kyoto
Osaka
Nara
Hiroshima and Matsuyama
I know it might be a bit too much, and I am still planning the trip because it will be next year and I still have time, but anywyas, other than the 14 day JR Pass, do I need to get any other pass for in city transport? Or is the JR Pass enough? And if I need extra passes, which ones?
Thank you.