What is the best route to Kyoto?
If you are traveling from Kawaguchiko to Kyoto, the most convenient route is Kawaguchiko Station → Mishima Station → Kyoto Station.
Travel from Kawaguchiko Station to Mishima Station on the Mishima–Kawaguchiko Liner Express Bus (reservation required), then take the Tokaido Shinkansen from Mishima Station to Kyoto Station.
If you can catch a Hikari Shinkansen from Mishima Station, your travel time may be shorter than going back toward Tokyo first and then traveling to Kyoto.