How to choose the best train option

Hello JRPASS team

We are a couple, planning 21 days in Japan, 6 days in Tokyo and 15 days includes Hakone-Takayama-Kawasama-Kyoto-Nara-Hiroshima-Okayama-Osaka-Tokyo (flight home).
In Tokyo we will use the metro/bus/regular train.
For the 15 trip day, I read that the JR pass can be expensive and not always the best option, because we plan to stay sometimes 2-3 days in one place.
How can I compare the regular train fees VS the JR tickets in order to choose the economic and best option?

Thanks a lot
Sharon