A Mt. Fuji/Hakone stop will be an early morning decision based on weather in mid-June. If it looks good, here is what I am considering. Please let me know if these routes are feasible, worth it, a waste of time, too much time sitting on trains/buses or we should just enjoy the view from Shinjuku to Kyoto without stopping. Would like to get to Kyoto at a reasonable hour, preferably before dark.
Shinjuku to Kawaguchiko
Kawaguchiko to Mishima Station via Fujikyu bus to Kyoto
Shinjuku to Shin-Fuji
Shin-Fuji to Kyoto
Shinjuku to Odawara
-Mt. Komagatake Ropeway and Lake Ashi
Mishima Station to Kyoto