A 2 week JR Pass, as suggested, would not pay off if you're only going to see the Tokyo and Kansai areas.
So you have 3 choices, all of which have some merit. One is to divide your time half in Tokyo and the other half in Kansai, and get a 7 day JR Pass. You can see Tokyo and nearby areas, then activate it just before going to Kansai, and return within a week (assuming you're leaving out of Tokyo again). There are many places near Tokyo worth seeing, including Kamakura, Nikko, Hakone, the Fuji 5 Lakes area, etc. You can also get some regional passes for some of them - see:
http://www.japan-guide.com/e/e2357.html Another choice would be to get the 2 week pass, and extend your itinerary. If you went to Hiroshima for a night and saw Miyajima (one of Japan's best places) and the city, that would make the 2 week pass worth it.
You could even go down more to see Iwakuni - it has one of the most famous bridges in Japan:
https://www.youtube.com/watch?v=0COOZXi66mMOr see Okayama - Korakuen is a beautiful garden there. Nearby Konpirasan in Kagawa makes a wonderful day trip and a fantastic mountain walk to a splendid view:
https://www.youtube.com/watch?v=ley9rVIewoQ One other choice if the above doesn't appeal to you is fly Tokyo-Kansai - there are many low cost carriers like Skymark, Jetstar, Starflyer, and Peach. Or ANA has a special fare too:
http://www.ana.co.jp/wws/us/e/wws_common/promotion/experience_jp/BTW since you'll be in Kansai, don't miss Nara either - it is a must-see place. You can see a lot of Kyoto in the day, then when the temples/shrines close about 5PM you can zip over to Osaka for the evening. There is a lot at night, such as Dotonbori:
https://www.youtube.com/watch?v=COJ_MeXbeowas well as the Umeda & Abeno Harukas Bldgs:
https://www.youtube.com/watch?v=xb1wuyAGgyQhttps://www.youtube.com/watch?v=-AyUZmGbW8gKyoto is the jewel of the area though. Some places like Kinkakuji you can easily see in half an hour; but other places like the Fushimi Inari Shrine can easily take half a day to explore:
https://www.youtube.com/watch?v=EandKTAwfOM In any case, there is a lot that awaits you.