The train journey to Takayama is quite scenic in places, so it's something to look forward to - whether you take the direct train from Kyoto or travel via Nagoya.

Any itinerary that includes Takayama is going to take a little more effort than a highly efficient circuit around Shinkansen stops. I think that the relative inaccessibility of Takayama is fundamental to its allure. Had it been on the coast or within the orbit of a major city, it wouldn't have such a well preserved historic quarter.

One idea if you want to see something of rural Japan between Takayama and Kanazawa would be to visit Shirakawa go - a village of thatched houses in the mountains - whether for a few hours or an overnight stop. There are tourist buses between Shirakawa go, Takayama, and Kanazawa.