Two weeks is not really that much. I assume you'll be in Tokyo area, Hakone maybe, with a few days in Kyoto/Nara/Osaka, maybe a day trip to Hiroshima? Then yes, someone suggested jr pass, you can't take Nozomi shinkansen but that's not a big deal.. you need to pay attention on which other shinkansen you take as the travel time say to Osaka varies considerably (can even double!) depending on the number of intermediate stops.

With the jr pass you can take metropolitan Tokyo jr lines, which are enough imho. Never felt the need to take the metro.

If you plan to stay in the Osaka/Kyoto area there's a kansai area pass, or the kansai are+Hiroshima (slightly more expensive). Very good deal because you can take also Nozomi shinkansen between Osaka and Hiroshima... pay attention though to get off in Osaka and take a normal train for the final osaka-kyoto leg if you are travelling Hiroshima to *Kyoto* instead, otherwise you'd have to pay the fare difference in order to exit the station gates.

Pity you don't have time to go to Kyushu because it's amazingly beautiful, but then you'd have an excuse to go back, and Kyushu deserves time and a dedicated trip imho.

Enjoy!