Certainly the JR pass does save some money, and is a good deal.

It's ok for the Tokyo area since it does have a good JR network in central tokyo (assuming your hotel in Tokyo is on a JR line in Tokyo). Essentially not very good once in Kyoto , where buses and non JR systems cover the city pretty well (If you need to travel around Kyoto, I suggest picking up a city bus pass for 500yen, a great deal, pays after 3 trips). I think I only used JR trains once in Kyoto itself.

For future visitors to this thread looking for information from Tokyo-Kyoto (and other info):

Lets say someone didn't have a JR pass and wanted to do Kyoto-Tokyo (RT or one way) only (say, one didn't have a JR pass because of Visa status in Japan/ or someone wanted to see if they can travel by Shinkansen but still want to save some money and not take slower overnight highway bus or local/night trains ), then a discount ticket to kyoto and back can certainly save money and sometimes a substantial amount of money (depending on how you travel), I listed one such discount plan here:

http://www.flyertalk.com/forum/showthread.php?t=725807

Btw I hope you enjoy the trip, if you can sit on the right side of the train going from Tokyo to Kyoto and you might be lucky enough to see Mt. Fuji (but it depends on the weather, clouds etc).