Best connection Tokyo - Kyoto
score:9
The fastest way is by Shinkansen - anything else is much slower.
Highway buses can be less than 5000 yen (one way), but take over 8 hours.
The cheapest (reliable) option would be the Seishun 18 ticket, which allows 5 (unconnected) days of unlimited travel, but only using local trains. Partially used tickets can be resold, so it comes out to 2300 yen (one way). The downside is that it requires changing trains a lot, takes 9 or 10 hours from Tokyo to Kyoto, and is only available/valid during summer and winter holiday seasons - so not applicable to you at all.
A 7 day Japan Rail pass is at 28,300 yen a bit more expensive than a Tokyo-Kyoto roundtrip by Shinkansen, but if you do any more travelling, it quickly pays for itself. It is valid on all JR lines, which includes some importnat local lines like the Yamanote and Chuo in Tokyo, but not the Tokyo Metro.
Upvote:4
The fastest way is by Shinkansen - anything else is much slower.
No, flying will be just a tiny bit slower, but also cheaper. This is especially true if one arrives at NRT and wants to go to Kyoto immediately. Then just hop on a Peach or Jetstar flight to KIX, and take the Haruka to Kyoto (with the massive discount offered by the Icoca & Haruka package). This may even be faster than N'EX + Shinkansen, and will certainly be much cheaper.
From central Tokyo, it will be less immediately advantageous, since flights from Haneda are a lot more expensive (and going to Narita costs both time and money), but it's a tradeoff. It comes out slightly cheaper, but also significantly slower.
For overnight buses, see Willer Express.
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