Japan Transportation Help

Hi there,

My partner and I will be travelling to Japan for 25 days.
Of that time we will be spending 6 days in Tokyo, then off to Kanazawa, takayama, kyoto (another 6 days), Nara, Hiroshima, Miyajima, Osaka, Hakone then back to tokyo for departure.
I realise the JRPass will be best for majority of the travel, but I am slightly confused for a few of the locations and around Central Tokyo. Will the pass cover travel on most of the local train networks or would it be Ideal for me to locate an alternative source such as the Pasmo service?

Many thanks!
Mik