Hi,
you may also consider Ise in your trip. The temple (more or less the heart of Japanese
shinto) has a very special atmosphere. It can easily be visited as a day trip from Kyoto, Osaka, Nara or Nagoya.
You may also want to spend half a day in Uji for the Byodoin,
Ise shrine and a few others (without mentioning the outstanding green tea).
While you may not want to go to the Tokyo region if you are in Japan for only two weeks, Kamakura and Nikko are definitely worth the visit. I would recommend you also spend a day in the countryside, for example north of Kyoto.
As a modern town, I would think Kobe is also very interesting, definitely worth a night out there.
If you can affort it, I would definitely recommend you spend one night in Nara Hotel, one of the few "Classic Hotels" in Japan built 100 years ago. You will find a few pictures and more details at this link:
Atmospheric hotels from Meiji era