If it's your first time and you want to visit Kiso and Takayama instead of warmer Ise Shima or Izu, I think cutting Tokyo is better to make another day for Kyoto. Actually, you can spend 10 days in Kyoto to see both old and new, quaint town and busy street. You might pick one either Kiso or Takayama to feel not rushed. Osaka and Nagoya can be skipped. I might even do just 2 full days for Tokyo, One day for Tsukiji, Asakusa, Ueno, Akihabara and another for Shinjuku, Harajuku, Roppongi Hills and Shibuya. If you feel like seeing department stores more, you can always see Isetan at JR Kyoto station.