For most people, Nagoya is a day stopover between Osaka/Kyoto and Tokyo. If you are very limited on time, fair enough, but otherwise there is more to see (3 days worth actually). If you go through Nagoya and do not stop to see the Maglev Train Museum, you are definitely doing it wrong :) We got up from in Kyoto and directly went to Nagoya, where we were going to spend one night. I chose a top floor room with view at the Marriott in the main train station, which turned out to be a great call: We then started with the Nagoya Castle. It's not the best castle to visit in Japan due to its renovation going on, but still worth a visit if you're there:
San Francisco could learn a thing or two about this and rebuild 101