The first time I went to Japan I tried to see everything. Two weeks, nine cities, a rail pass that I wore around my neck like an Olympic medal. By the end of it, I could tell you which shinkansen stations had the best ekiben bento and nothing about what any of the nine cities actually felt like. That was a mistake I've spent every return trip correcting.
The country is built for slowness. Every city contains enough neighbourhoods, backstreets, teahouses, and 7-Eleven-at-2-a.m. epiphanies for a month; the moment you try to compress that into 36 hours per city you stop seeing anything at all. The second time I went, I spent ten days in Kyoto and came home having understood more about Japan than my entire first trip.
Three rules
Rule one: no more than three cities in a two-week trip. Rule two: at least three full days in each. Rule three: one day per city with nothing on the itinerary at all. Those three rules will save you from the collective delusion that a tightly-optimised travel schedule is somehow better than an open-ended afternoon in the same neighbourhood.
The other thing: take local trains where you can. The shinkansen is an engineering miracle and a fast way to skip Japan. A local train from Kyoto to Nara through the rice fields will teach you more about the country than a bullet train to Osaka, and it only costs you ninety minutes.