I have researched this quite a bit and I think I understand it but wanted to ask something I can't find the answer to:
I am spending my first 6 days in tokyo then the second week doing Mt Fuji, Kyoto, Hiroshima, Osaka
Is it worth getting a Rail Pass for the full two weeks or only for the second week and pay as we go in Tokyo?
I know the RP can be used to get around Tokyo but do you also have to use and pay for the subway or are the trainlines sufficient?
If money is an issue than personally I'd get a one week rail pass.
I'd spend the first week using the pass and validate it right in Narita (I am assuming that's where your flying into). I'd utiilize the pass to travel from Tokyo to Kyoto, Hiroshima, Osaka. Then at the end of the week I'd head back to Tokyo. If I wanted to stay longer than 7 days outside of Tokyo, I'd get my traveling done first then spend the extra days after the pass expired in Kyoto and book an overnight bus from Kyoto to Tokyo. Then I'd go to Fuji during my stay in Tokyo. Finally when heading back to Narita I'd save a few bucks by taking the Keisei line instead of the Narita Express.
In general, you'll probably prefer buying subway tickets in Tokyo than relying on the JR line.
I'm going to Japan on September the 15th and i have decided to get the JR pass, i'm staying in Japan for 4 weeks and will get the 21 day pass. I've decided to "activate" the pass when i'm leaving Tokyo after the first week spent there because as i have understood it, the subway lines that the pass works on in Tokyo doesn't cover all that much.