Sarra, if you take one of the 3 Mt. Fuji trails originating from Shizuoka Prefecture, those trailheads can be accessed from both Mishima Station and Shin-Fuji Station on the Tokaido Shinkansen (bullet train) line, providing a direct high-speed connection to Nagoya, Kyoto, Osaka, and all points south.
However, coming from overseas, I assume you'll use the main Yoshida route, and because it lies on the northeast side of Mt. Fuji, to my knowledge there's no easy way to get from there to the shinkansen line without going back into Tokyo. More trail access details here: http://www.fujiyama-navi.jp/fujitozan/access/page/bus/lang/en/
If you're definitely planning on traveling south after scaling Mt. Fuji and you'd like to escape the crazy crowds you'll find on the Yoshida route, :-( I'd encourage you to consider the Fujinomiya route which I climbed up just 2 years ago. Here is my report, including pics, maps, video, and trail description: Climbing Mt. Fuji's Fujinomiya Trail
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