I'd choose to go to Nagoya, mainly because it's the area I'm most familiar with, given that I lived and studied there for half a year. It's definitely less congested than Tokyo, and the Meitoh neighbourhood is filled with shops that sell you everything at cheap prices - comics, food, trinkets, whatever. And Nagoya isn't short of traditional heritage either - there are several temples (even though they're not the most famous ones) and there's the Tokugawa Art Museum, and Nagoya-jou, which I think is a work of art.
It'd be nice to go to Kyoto too, because when I went there I found the food there pretty cheap. And I didn't manage to go see all the temples I'd have liked to see, even though I've been there like, thrice. And this might sound silly, but I want to go to Osaka so I can hear people speaking Kansai-ben. It fascinates me because I suck at it ^^;;
There are loads of nice places to visit in Japan. I had a hard time settling on these three states +__+