First time visit and hence many basic questions

We (family of 3) would be visiting Japan in mid April and this is how the schedule looks like:
9th April - Land in Narita at 730am. Hotel booked in Shinjuku. Local site seeing
10th April - Local site seeing. Maybe Hop on Hop off tours
11th April - Visit to Disney waterland (have a son of 15 years)
12th April - Check out and visit Mt Fuji. After seeing Mt Fuji, proceed to Hakone. Night stay at a Ryokan in Gora
13th April - Site seeing
14th April - Hakone to Kyoto
15th April - Site seeing to Nara
16th April - Local site seeing
17th April - Hiroshima
18th April - fly out from Kansai Airport, Osaka. Flight time 1030am.

My questions:
1. Is this a good itinerary for a first time visitor? Any suggestion to improve will be really helpful
2. Do you recommend us to buy a JR pass?
3. For the departure, what would be the suggestion - should we go from Hiroshima to Osaka or come back to Kyoto and on 18th morning go straight from Kyoto to Osaka airport?

Cheers