Itinerary for 2 weeks in Japan

Hello,

I recently posted a question about how economical a JRPass would be for our trip to Japan which is actually 2 weeks from April 3-17:

Tokyo - 5 days (includes arrival)
Kyoto - 4 days
Osaka - 4 days
Tokyo - 5 days (includes departure)

Of course we plan to do some sightseeing (shrines, parks, temples) in the city and visit theme parks such as Disney Sea and Universal Studios since it is our first time. We plan to do Mt. Fuji and Hakone as well. However, I was advised that we may not be getting the most out of our JRPasses if we just stay in the City. Could anyone give me some advice on what an ideal itinerary looks like for 2 weeks considering the itinerary we have now? Something that could probably make getting JRPasses worthwhile for 7 or 14 days?

Sincerely,

Lisa