2 full days in Kyoto is definitely not enough. The Golden Temple, hiking the Philosopher's Path and visiting many of the temples along the way, Fushimi Inari (my top Kyoto highlight), dining, shopping and I didn't even make it to Arashiyama. I would definitely take a day off of Tokyo and add it to Kyoto.

I didn't get to Takayama but did spend a day in Matsumoto and another day in Kamikochi. The castle is far and away the highlight in Matsumoto (but oh, what a highlight) and I spent the rest of that day enjoying the gorgeous fall colors (it was November), visiting the Kaichi Elementary school, wandering the town and eating delicious pork ramen and enjoying an ice cold Kiren in the chilly fall air. (The waitress thought I was a bit crazy having lunch outside but being from Minneapolis, 50 degrees and sunny was beautiful and refreshing.) If you can squeeze in one day for Matsumoto, I think you'll find the castle to be one of the highlights of your trip.

I've been to both cities during a 3 week Japan trip and , as others state, your interests should guide your decision. Any way you slice it, I,too, would advise more time in Kyoto.