You should spend time in Tokyo and Kyoto. Also if you have chance, take a stop in between for a night or two at an onsen in Hakone or somewhere else in the Izu. Maybe a daytrip from Tokyo to Kamakura.

A two week JR pass will be perfect for you which will allow bullet train travel between Tokyo and Kyoto. Make sure to time it right so that you can acitvate your pass on arrival at Narita and use it on the 14th day to return to the airport.

Given 14 days via the pass we're talking 13 nights: You arrive on day one and activate the pass and get to your hotel in the early evening.

You could spend nights 2-5 in Tokyo, 6-9 in Kyoto, 10-11 at a hotspring, 12 in Hiroshima if you like (because you can get ther for free on you JR pass), and you still have an additional Wild Card night for Tokyo on you way back.

Have a nice Day.

Scho