We will be in Japan for two weeks. The first week we will stay in Shibuya, but the next week plan to travel from the Shibuya area to Kyoto and Osaka, and then come back to Shibuya.
I see the Kyoto area pass is $20 to travel in that area. So, is there another pass or train we will take to get from Shibuya to Kyoto?
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If you have the JR Pass, you won't need any regional rail passes like the Kansai Area Pass - although some city passes like the Osaka Amazing Pass or the 500 yen Kyoto city day bus pass can help you save a lot. The Kansai Area Pass would not pay for itself anyways unless you did a long trip like to Himeji.
Since you are already seeing Tokyo, you can largely skip Osaka during the day. After the temples of Kyoto close down around 5PM, you can zip over to Osaka for the evening. At night the city comes alive and has some great places to see, such as Dotonbori, plus the night views from the Umeda Sky Bldg and Abeno Harukas Bldg are wonderful.
Also IMHO for Tokyo 3-4 days are quite enough. Use some time to see some good places nearby, like Nikko, Kamakura/Enoshima, Karuizawa, Izu, Kusatsu, and for Mt Fuji there is Hakone and the Fuji 5 Lakes area. A Tokyo Wide Pass could save you a ton, and for near Mt Fuji there are good regional passes too.
http://www.odakyu.jp/english/deels/
Within Tokyo there is a good 3 day subway day pass.
http://www.tokyometro.jp/en/ticket/value/travel/index.html#anc03