Osaka-Kyoto-Hakone-Tokyo

Hi,
We are planning to fly into Osaka spend 2 days touring there, maybe going to Nara.
Next travel to Kyoto for 2 days of touring.
Next we go to Hakone for 1 night- hoping to take Bullet train there then use local trains to see sights.
We may stop in Hadano for a hike & yoga on the way to Tokyo.
Our final stop is 3 nights in Tokyo before departure out of Haneda to the States.
I looked up trips from city to city (excluding Nara) & JR pass was not recommended but I am wondering if the ability to use within cities, especially Tokyo where we are staying in the Ginza district would make it cost effective? I have read about Kansai passes & Hakone pass, would they be a better option?
Thank You!