Which pass to get?

Hi,
A 14 day pass would pay off for your plans. But given that you are in Japan for 15 days (counted midnight to midnight, for using a rail pass) you would need to pay out of pocket either from or to Narita Airport. Fortunately there are cheaper ways now, such as on the 1000 yen bus.
Within Tokyo you could use the pass to ride the Yamanote Line within the city - it goes to many popular tourist places. In total it doesn't add much value, but everything counts. You could also use the pass for a day trip to Nikko, which is well worth seeing.
You could spend a lot of time in Tokyo and still not see everything.
In Tokyo a few of the best places to see are the Tsukiji Fish Market, plus the site that every last tourist goes to see, the Sensoji Temple. If you are in Tokyo on a Sunday afternoon, be sure to go visit Harajuku to see the youth with their wild fashions. Meiji Shrine and Yoyogi Park are next to it and well worth seeing also. And be sure not to miss the Shibuya Hachiko intersection especially on a weekend when it looks like half the city is crossing the street at once.

You could expand your value further near Kyoto by taking at least half a day to see Himeji which has Japan's finest castle. Nara is also a must-see place in the area. Nara is often neglected by some tourists, which is a shame. Missing the Todaiji in Nara is like going to India and skipping the Taj Mahal. Nara Park has a lot of great places. A few other great places missed out even by those who go to Nara though are the Isuien and Yoshikien Gardens. They are gorgeous and not crowded at all.

Best of luck.