I believe your itinerary is a bit rushed.
You could perhaps skip Nagoya.
If you stay in Kyoto, you can visit the cities around like Nara and Osaka, since they are not so far away, you can go by regular train.
And from Tokyo, you can go to nikko and the ski station. Just mind the crowds during the weekends. If you have the opportunity, it is better to visit the ski stations on weekdays