I'm also still a bit confused with Shinkansen reserved vs. unreserved. A Shinkansen charge on a ride without seat reservation for Odawara -- Kyoto is 4920 yen. If you use a seat requiring reservation, this charge is a bit higher by 310 to 710 yen, depending on seasons and days.
(You can pay the gap and switch to a reserved seat if there is vacancy, but you cannot do the reverse.)
You will hold both a base-fare ticket and a Shinkansen ticket for your Shinkansen ride.
A train on Tokaido Shinkansen is composed of
Ordinary-Class cars with seats used without reservation,
Ordinary-Class cars with seats requiring reservation,
and Green-Class cars (called "Green Cars").
A Green Class is a higher class. If you are in a Green-Class car, a Green-Class charge is required even if you do not have a seat. Please pay attention to car numbers.
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http://www.japan-guide.com/e/e2018.htmlI have heard that some of people who are living apart from families for commuting to a workplace use Shinkansen to go home and come back in weekends.
Business persons can make a daytrip using Tokaido Shinkansen between two offices located apart in two of Tokyo Metropolis, Nagoya City and Osaka City.
Tokyo to Hakone (Odawara Station?). Do I need another one for Tokyo-Odawara? Hakone area is not served by JR companies.
You can get to Odawara either by Odakyu or by JR.
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http://www.japan-guide.com/e/e5206.htmlYou will stay in Hakone area for at least one night. So, a Hakone Free Pass issued by Odakyu may be a good choice.
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http://www.japan-guide.com/e/e2358_008.html(You will not head back to Tokyo, so an inside-the-area edition will be enough.)
I won't be heading back to Tokyo and will instead go straight to Kyoto afterwards. Then it sounds good to pay a base fare either of 6830 yen for Odawara Station -- Kyoto Station or of 7350 yen for Odawara Station -- your JR station in Osaka City. The base-fare ticket will be valid for 4 calendar days. (Kyoto and Osaka are connected by JR and non-JR lines.)
A base fare is a fee required regardless of trains / classes. If you take a train on Shinkansen / a Ltd. Express train on a non-Shinkansen Line, a service charge is required in addition.
Your route to KIX depends on the location of your Osaka hotel.
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http://www.japan-guide.com/e/e2033.html