We are traveling to Japan for 3 weeks. 1 week in Tokyo, 1 week in Kyoto, 1 week in Osaka. We thought we would get we get a 2 week pass validating it after our week in Tokyo and to do day trips from Kyoto and Osaka. It has been suggested to me that I should get a 3 week one and use it in and around Tokyo as well? Also it has been suggested that we purchase a Green pass as the carriages are less crowded, but is this really necessary as it is very expensive. We are travelling in October. If we only buy a 2 week pass what is the most economical way to get around Tokyo?
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October is a popular time to travel in Japan since the weather is very pleasant in autumn, however the trains should not be so crowded that you need to worry about getting a seat without using a Green Pass. A regular JR Pass should be all you need.
If you are staying in Tokyo for a week without making many trips outside the city, the JR Pass will not save you much money on travel there. You can use local JR lines such as the Yamanote line, but the Tokyo Metro is not covered by the pass, and buying individual tickets or using a Pasmo or Suica card (https://www.japan-rail-pass.com/common-questions/what-is-a-pasmo-or-a-suica-card) would almost certainly work out cheaper than the extra cost of a 3-week JR Pass. A two-week pass for use after your first week in Tokyo sounds like the best option for you.
There are a few discount tickets available for travel around Tokyo, Japan Guide gives a good rundown here: http://www.japan-guide.com/e/e2017.html
I hope this helps.
Sincerely,
Japan Experience
Alternatively you could cut some time off of the Kansai area and with a 2 week pass do some good day trips in the Tokyo area (Izu, Nikko, Karuizawa, Kusatsu, for example).
Actually, a whole week in Osaka is serious overkill, particularly if you are already seeing Tokyo. Every place has something to see, but your time would be better used with other places. Nara is a must-see place, and you can also spend a day to see Himeji, with Japan's finest castle. Kobe is also worth a look, and if you'd like to see the more spiritual side to Japan, you could go and spend a night at Koyasan in Wakayama.
http://www.japan-guide.com/e/e4900.html
You could save Osaka for the evening after seeing Kyoto. Osaka comes alive at night with great places like Dotonbori, and the night views from atop the Umeda Sky Bldg and Abeno Harukas Bldg are stunning.