short vacation in japan

I plan to start using JR pass from 10/7 from tokyo to osaka, i have until october 12 to return to tokyo and would like
to visit different cities like kyoto, hakone, or any popular tourist spot on the way and need some advise where
to stay like overnight stay in kyoto, osaka or kobe...
a nice itinerary or schedule will be great.

any advise will be much appreciated, using our JR pass, my wife is first time in Japan.

Sincerely,

Rvalenciano