Starting and ending your climb at Shin-Fuji Station is the best logical option. From Shin-Fuji Station you can easily access Bullet Trains South to Kyoto or Osaka, or North to Tokyo or even to Hakone.
The pictures to the left shows sample itineraries of how to get from:
(1) Tokyo Station to Shin-Fuji Station (70 min)
(2) Shin-Fuji Station to Kyoto Station (105 min)
(3) Shin-Fuji to Hakone Yumoto Station (41 min)
All these routes are fully covered by the Japan Rail Pass. You can find your own itinerary by accessing this link here.
This is by far the fastest route to get to Tokyo or to Kyoto from Mt. Fuji. Starting from Gotemba Station only adds to your travel time as you have to transfer to a Bullet Train Station anyway using a local JR train line to get to Tokyo or Kyoto.
Getting dropped off at Shin-Fuji Station is also the best option if you're heading to Kawaguchi Lake, as there are four daily buses that run between the Kawaguchi-ko Station and Shin-Fuji Station using the less crowded local road running behind Mt. Fuji: See Bus Timetable link below:
Shin-Fuji Station to Kawaguchiko Station Timetable
So why take the long way from Tokyo and get stuck on the overcrowded highways when a fast-spacious Bullet Train option is readily available?
All My Tokyo Guide Mt. Fuji tours and climbs will offer Shin-Fuji Station pick-ups and drop-offs for quick, easy, painless Mt. Fuji transfers.
My Tokyo Guide