Although you are still assembling the puzzle of the route, we will most likely go from Tokyo to Kyoto directly. As I still do not know if it will be at the beginning of the trip, and taking into account that of the 20 days we will be there we will only have Japan Rail Pass For 14 (because it's two weeks), I've been looking for the cheapest way to go. The train is completely discarded, a ticket from shinkansen It comes out for about 13,000 ¥. But then I remembered the night bus trip that Azuki and I did the previous time. The good thing about the night bus is that it is cheap and you also save a hotel night. The bad thing is that you arrive made dust.
The shinkansen or bullet train
JR BUS has two bus lines that run from Tokyo to Kyoyo. The Seishun Dream leaves for about ¥ 8180 and lasts about 7 and a half hours. There is also the Seishun Chuo Dream, which lasts 8 hours and leaves for ¥ 5000. In the first, if you buy the ticket 21 days in advance they give you a 35% discount and in the second a 15%.
However, searching online I found a website called 123bus.net. Here you can buy on-line the ticket, choose between different types of bus (with or without bathroom, more spacious, etc.). The cheapest ticket is the one that leaves at midnight (23:10 - 07:00) and costs ¥ 3900. You can also buy passes to travel around Japan by bus Willy Express.