Here is the sample Itinerary for a 2-week trip to Japan. You can plan your trip along these suggestions.
Day 1- Land at Tokyo or Osaka depending on the flight and spend a day at the city.
Day 2-3 Move to Kyoto- Spend the day visiting the shrines Fujishimi Inari Taisha Shrine , Ryoan-ji &Ninna-ji Temple and the Gion area. Read what to do in Kyoto here
Day 3-7- Head to Osaka to catch flight to Okinawa Naha. Spend the evening at Naha. Next morning catch a morning ferry to Zamami Island. next few days enjoy the serenity and beauty of Zamami and nearby islands. Read more about these Islands here
Day 8-: Catch Ferry back to Naha and Flight to Tokyo. Spend Night in Tokyo.
Day 9- Leave early for a day trip to Mount Fuji. Spend the day around Hakone to enjoy Mount Fuji and head back to hotel in the evening. Read about Mount Fuji here
Day 10-13: Spend the day visiting various Tokyo gardens and watching Cherry Blossoms.This day is for seeing the various parts of Tokyo. Visit the various temples, shrines, Shibuya crossing, Shinjuku area and head to Akihabara for some electronic shopping. Read about all you can do in Tokyo here & here
Day 14- Checkout from hotel and back to your destination