14 days JR Pass or individual tickets

Hi,
It would pay off including the extra charge for reserved seating, plus on top of that there is the convenience of not having to constantly go and buy tickets at every major station.
But you are missing a few good spots that would also increase your savings. While in the Tokyo area, take a day trip to see Nikko and Kamakura. The Pass is still valid so you can save even more. You can also use the Pass to take the JR Yamanote Line, which is not expensive in itself but is covered by the Pass and goes to many popular tourist areas. Also Fukuoka has a number of great places to see if you can fit them in. The Nanzoin Temple is a hidden jewel that few have even heard of, yet it one of the best temples you will ever visit in the country:

https://www.youtube.com/watch?v=lT4VQFmHFyM

For other ideas of what to see, look at:

http://www.thejapanfaq.com/fukpic.html

Generally one day is enough to see Hiroshima City, and 1 day for Miyajima works well too.

You don't say when you are traveling, but hopefully it will be after the Himeji renovations are completed. Also you can zip over to Osaka when the temples and shrines in Kyoto close around 5PM to enjoy the night life. Dotonbori is a great place for food and the Osaka atmosphere.

https://www.youtube.com/watch?v=COJ_MeXbeow

Sounds like a great trip.

Dear Toraneko,
Thank you for your very useful comments.
I am arriving at Naha, Okinawa on May 8, 2015 and flying to Fukuoka on May 11.
Never thought of quick round trips from Kyoto to Osaka. Definitely will consider them now.
I'll stay 6 days in Tokyo. Have already been to Nikko in a previous trip to Japan. A day trip including Kamakura and Yokohama sounds very interesting. Will look into it.
Best Regards

If you've been to Nikko, then Hakone is another possibility. There are some great views of Mt. Fuji when the weather cooperates, and if it doesn't there are still enough interesting things to see and do there.

http://www.japan-guide.com/e/e5200.html

http://www.japan-guide.com/e/e2358_008.html

Dear Toraneko,
Thanks again for your advices.
Best Regards