2 weeks in Japan - october 2014

Hi
me and my husband will be in japan for 2 weeks for the first time.
the itinerary:
landing in Osaka, taking train to Kyoyo - 5 nights,
Hiroshima - 3 nights, going from there to Miyajima for 1 day.

Tokyo - 5 nights.

My question is what are the must places we should see in these areas.

I'm confused and cant decide.
we will buy the jr tickets for 2 weeks.

Need your help.
Thank you

It seems to me that there isn't a need for the 2 weeks JR Pass, unless you don't want to queue to buy train tickets. Because the cost of the JR Pass is not covered by the cost of your travels.
You don't need a JR Pass to travel within cities

You might want to spend some time in Osaka for the cheap/good food. But considering attractions and the city experience, Tokyo covers that.

For Kyoto, you could allocate each day for a part of Kyoto
Day 1 Northern: Ryonanji/Golden Pavailion
Day 2 Western: Arashiyama/Takao/Daitokuji
Day 3 Eastern: Gion/Higashiyama/Philosophers path
Day 4 Central: Imperial Palace/Nishiki Market/TeramachiDori
Day 5 Southern: Fushimi Inari/Tokufuji

If you walk fast and see attractions fast you can do more than 1 area in a day. But the slow zen of Kyoto is one reason not to rush things

If you do have time, make a 6 hours trip to uji. Most people would say Nara but if you wanna see deer. please go to a zoo/safari or Miyajima

Hiroshima truly, doesn't have much to do
But if it is your virgin trip to Japan, seeing a castle for the first time counts for something.
Rent a bicycle at Hiroshima station.
Cycle to the castle, to the park, to the atomic bomb museum and peace park.
Eat the Okonomiyaki
Spend a full day in Miyajima. Eat the street food.
You could take a trip out of Hiroshima into Okayama if time permits.

Tokyo
Shop at Shibuya/Shinjuku
Peace out at Meiji Shrine
Crowd at Sensoji
Unless you can shop nonstop and finding trendy cafes is your thing... 5 days is too much

Thank you.
I see that many tourists go to Takayama. is it worth?
what side trips can we do Kyoto?

Hakune or Nara?

The use of the Jr is not for train from Osaka to Kyoto? and from tokyo outside to other areas?
Thank you