Itenerary check - 17 days

Hi,

My partner and I are travelling to Japan in June and this is what our itinerary is looking like:

Day 1 - 3 - Tokyo
Day 4 - Disney Land
Day 5 - Travel to Hakone and spend the night in a Ryokan
Day 6 - Explore Hakone and travel to Kyoto
Day 7 - 10 - Kyoto (Day trip to Arashiyama and possibly Nagoya)
Day 11 - 13 - Hiroshima (day trip to Miyajima)
Day 14 - 15 - Osaka
Day 16 - 17 - Tokyo

My quetsions are:
1. Would you reccomend using the JR Pass around Tokyo? Or would it be better to purchase a three day metro ticket and then getting a 14 day JR Pass rather than 21?
2. Would you recommend getting the Hakone free pass?
3. Will all other trips be covered on JR pass?

Thanks you!

Olivia