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Tokyo - Kyoto - Osaka (20 days)

I will be spending 20 days total in Japan with 10 days in Tokyo, 5 in Kyoto and 5 in Osaka in that order.

First of all, all my activities there are just tentative, aka free roam most of the times. I'm prepared to use Suica/Pasmo card for bus fair and misc spending. Among the places I planned to go in Tokyo are Ikebokuro, Akihabara, Shinjuku area, Shibuya, Odaiba, and others. Will be staying around Kodemmacho during my time in Tokyo, Shimotsubayashi(Nishikyo Ward) in Kyoto and Shimoshinjō(Higashiyodogawa Ward) in Osaka.

Tokyo Wide Pass only covers 5 days and Kansai Wide Pass also 5 days. I doubt that 21 days JR Pass is worth the money since I will probably not use trains all the time(correct me if I'm wrong). However I will need to get a ticket for Shinkansen from Tokyo to Kyoto. Should i get multiple 1-day Tokyo pass?

Which pass(es) suits best for my needs?
Appreciate your kind assistance to enlighten me in my decision making.

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    edited February 2017
    You are completely correct - you would lose a horrific amount of money on a 21 day pass just going to where you mention.
    BTW the Tokyo Wide Pass is good for 3 consecutive days, not 5.
    You only get good value on a JR Rail Pass with long distance travel, especially by bullet train.

    You have a few options. You could just buy regular tickets for the round trip between Tokyo and Kansai.
    Or, you could get a 14 day pass for the long distance travel to Kansai, and with a day trip or overnight to Hiroshima/Miyajima, you could make a 14 day pass pay off. Alternatively, a few day trips to places like Nikko, Karuizawa, Izu, Kusatsu, Sendai, Himeji, Kanazawa, etc plus the round trip would work as well.

    For a 21 day pass to pay off, you'd need to do both. But with the amount of time you have, you could see a large number of good places and really rack up some good savings.
    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.
    On another evening, you could also go and see Kobe.

    You should definitely not skip Nara, which has some of the best sights in the whole country. An overnight at Koyasan would also be an unforgettable spiritual experience. For that though, you'd save money on a Koyasan World Heritage Ticket.
    http://www.japan-guide.com/e/e4900.html
    http://www.japan-guide.com/e/e2358_012.html
    Taking the Hokuriku route one way and adding sights like Shirakawago would be a different experience as well.
    http://www.japan-guide.com/e/e5950.html

    For seeing the Mt Fuji area, one of the Odakyu passes would help.
    http://www.odakyu.jp/english/deels/

    You are making a common mistake though of picking a rail pass first and then making an itinerary. You should decide where you want to go first and *then* choose the best way to get there. I suggest you browse a site like www.japan-guide.com and figure out what interests you. There is a sample itinerary at
    http://www.japan-guide.com/e/e2400_tokyo_19.html
    but don't feel that you have to be tied down to the beaten path.

    You can see regular fares, routes and schedules on Hyperdia.
    http://www.hyperdia.com
    Under "More Options", be sure to uncheck the Nozomi box since you can't ride that train using the pass.
    This can help too: Japan Rail Pass Calculator
    http://www.japan-guide.com/railpass/

    For within Tokyo a 2 or 3 day subway pass can save money.
    http://www.tokyometro.jp/en/ticket/value/travel/index.html#anc03

    If you use a rail pass from Narita, the Narita Express train is a good way to add value. If not on a pass then the 1000 yen bus is the cheapest.
    http://accessnarita.jp/en/home/
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    Thank you so much for the very detailed explanation. Certainly helped a lot in some of my concerns.

    The thing is, I had a rough itinerary planned out. But opinions are greatly valued. And yours made me rethink a whole lot about my itinerary. Below was my original plan.

    Tokyo(10 nights): Within Tokyo, probably use Pasmo to go around the city. Plenty of things and places to discover, too many to summarize.
    Kyoto(5 nights): Arashiyama, Saganao, surrounding castles and temples (I think I listed 4 down). Originally wanted to drop by Kurama Onsen but the rail pass does not seem to include that. So I will need to find another onsen to enjoy.
    Osaka: Nara was top of the list here since it seems nearer from here rather than Kyoto. Probably rent a bike to go around the park. Then comes the parks and shrines, Bunraku theater and Dotonburi.

    I apologize if my opening post sounds vague. I didn't want the itinerary to be packed since i expect some downtime(laundry and rest). Provided that Pasmo also works for Osaka and Kyoto's buses, I may be inclined to get one-way ticket for both Tokyo-Kyoto and Kyoto-Osaka.
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