Kyoto for sure... take a short train hop to Osaka part of the time to get your big city fix.

I'd like to ditto #10. Why limit yourself to Kyoto or Tokyo? I'd stay in Osaka instead. Just walking around the Umeda area will wash all of that rural Japan right out of your head. Seas of people, tons of restaurants - from standing noodle shops to trendy spots (go to the top floor of any large department store for great views and food - not too expensive), and a ferris wheel poking from the top of a department store! - http://www.livehep.com/about/index2.asp<BR>In Google Earth, this area is at 34°42'13"N, 135°29'48"E
You can take JR from Shin-Osaka to Osaka, then walk around the area and get lost. Yodobashi Camera, just in front of the station (NE side) is overwhelming. The Umeda Sky Building is also cool - http://www.skybldg.co.jp/garden/e/index.html<BR><BR>If you stay near Shin-Osaka station, you can catch a quick train to Nagoya for your flight home. It's only 1:05 on the Hikari from Shin-Osaka to Nagoya.
This is a great new service in English for finding train times - http://www.japanrail.com/JR_timetableandfare.html<BR><BR>Have fun.