I will mostly be staying in the Kyoto area , but have been to Japan 3 other times so am fairly familiar with the train system. But how do I cover the rest of my stay by train? I don't think it is worth paying for another 2 week pass, especially since I already bought the green pass(my preferred way to go after trying both last June) and wonder if I should get a regional pass. can I get them in Japan as I want to have a flexible schedule.I would like to visit Hiroshima, and maybe up to Nigiita..Also is it cheaper to fly to Hokkaido than to use the train? I used th eJR pass last year but it was an all day ndeavor and had to change from bullet to limited express train in northern Honshu
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For people like you with a very long visit, or very slow travel pace, it is often better to use a series of regional passes than the full JR pass.
Unless you are traveling long distance, especially by bullet train, it is actually hard to make a rail pass pay off.
Nearly all regional rail passes you can get after arriving in Japan. However, with most JR West passes, you can only get one pass per visit if you buy it in Japan. If you buy the same passes before going to Japan, you can buy as many as you want and use them all, as long as they are used consecutively.
Flying to Hokkaido is so much better for your sanity than sitting on trains and murdering the whole day. If you toured your way up there, you could actually see and experience a lot. But if you just want to get up to Hokkaido, flying makes more sense. There are some low cost carriers that can take you for peanuts. Try looking at:
http://www.jetstar.com/jp/en/home
http://www.flypeach.com/pc/en
If you want another option, there is also ANA's Experience Japan Fare.
http://ana.ms/20Xtf8t
For regional rail passes, I suggest you browse what's available at:
http://www.japan-guide.com/e/e2357.html
You can see regular fares, routes and schedules on Hyperdia.
http://www.hyperdia.com
Under "More Options", be sure to uncheck the Nozomi box if on a full JR Pass since you can't ride that train using the JR pass. If a regional pass however that allows using the bullet train, frequently you can use the Nozomi.
You can see previews of some of the best places to see in Japan on:
https://www.youtube.com/user/thejapanfaq/videos
There are also loads of other tips on
http://www.thejapanfaq.com/the-best-japan-travel-tips/
Best wishes.
https://world.jorudan.co.jp/mln/en/japan-rail-pass/?sub_lang=nosub
I would use Google Flights to find an air ticket. The starting value is 5190 yen for KIX-CTS by JetStar.
https://www.google.com/flights/#search;f=KIX,ITM,21Y;t=CTS,OKD,23Q;d=2018-05-21;r=2018-05-21;tt=o
For Vanilla and Peach travelers, there are some offers by JR.
http://www2.jrhokkaido.co.jp/global/pdf/e-vanilla.pdf
http://www2.jrhokkaido.co.jp/global/pdf/e-peach.pdf
https://www.vanilla-air.com/en/
http://www.flypeach.com/pc/en
More promotions are here.
https://www.japan-guide.com/e/e2364.html
https://www.japan-guide.com/e/e2365.html
Have you checked 600 yen tickets by Peach (not 6000 yen) started to be sold on 2 Mar?
http://www.flypeach.com/pc/en/um/specials/sale/sale?www_pc_en-us_mini_banner_01
You may go to Hokkaido by ferry. A night could be saved. Akita-Tomakomai from 4530 yen and Niigata-Otaru from 6480 yen.
https://www.snf.jp/english.html
https://www.snf.jp/english/pdf/Tsuruga_Niigata_Akita_Tomakomai-higashi.pdf
https://www.snf.jp/english/pdf/Niigata_Otaru.pdf
http://www.taiheiyo-ferry.co.jp/english/
https://www.sunflower.co.jp/en/
https://www.directferries.co.uk/hokkaido.htm
https://www.japan-guide.com/e/e2355.html
https://upload.wikimedia.org/wikipedia/commons/f/f2/Tokyosapporotrainchart.png
https://en.wikipedia.org/wiki/Hokkaido_Shinkansen
Anyway, most people usually use a 21-day Japan Rail Pass for a month travel something like the below.
1) Kansai 10 days + 21-day Pass (Osaka in and out)
2) Kanto 10 days + 21-day Pass (Tokyo in and out)
3) Kansai 5 days + 21-day Pass + Kanto 5 days (Osaka in and Tokyo out)
In both Kansai and Kanto areas, private operators do good jobs. Even by JR, the fares should not be so expensive within the region.