I'm pondering the economics of the railpass myself at the moment.
Have a look at this site for prices and timetables (not just JR)
http://www.hyperdia.com/
click on the English button on the left.
(Hikari )Tokyo to Kyoto 13200 yen 1 way. (returns are 20% less than 2 singles I think)
so between 26200 and 21120 yen
Nagoya to Takayama is about 6000 1 way I think. Prices seem to have a direct relationship to distance. You pay per kilometre. Nozomi isn't covered by the rail pass but I don't think the 30 min difference is a big deal to holiday makers.
28300 --7 day pass.
45100 --14 day pass.
Do the math. To get full value from a 14 day pass you'd probably need to go down to Kyushu.
The other possibility, and I have no idea how feasible it would be, is to fly into Kansai but fly out of Narita (or vice versa). As long as this costs no more than flying in and out of a single airport, you would then probably have a cheaper time of it using rail as you'd only have a single shinkansen journey to make. Or you could do most of your train journeys on a 7 day pass in the middle of a 2 week trip.
I think however the temptation of a pass is to wring the most out of it. I had a fleeting idea of going from top to tip of Japan on the rail pass! 3000 km? Probably no time to stop anywhere! I might do it some day, but it'd have to be in style using the green pass!!
So the pass can be good value, especially if you go a bit further than Kyoto and Tokyo.
side trips to Nara, Osaka, Himeji, Kobe from Kyoto for instance. or kamakura and nikko from Tokyo not to mention the train between Narita and Tokyo. (I still think Kansai and Centair airports are worth investigating, as a more pleasant experience especially if you'll be using a rail pass and visiting Kyoto or Nagoya as well as Tokyo)
The other thing to bear in mind is that it cuts down on interaction with ticket offices if you are unsure of your Japanese. It can be a wave at the barrier experience rather than try to explain where you want to go, and have them try to explain the complexities of Japanese railway ticketing and transfers. Also if you are adventurous you don't have to plan it so much, you can get on and off trains on a whim.
I don't know Tokyo, but in Kyoto the main subway wasn't run by JR so therefore wasn't on the pass (nor my 2 day ticket, which was about 2000 I think for unlimited bus and subway) Buses are the best way to get about Kyoto I'd say. (Also just to mention in passing kintetsu seems to cover more of Kansai/Kinki than JR, so when I travelled in Kansai a JR pass wasn't economical for what I wanted to do)
You might want to read this guide. It's been revised recently so should be fairly up to date.
http://www.amazon.com/Japan-Rail-Ramsey ... 873756976/
I've used the first edition and it seemed good.