I agree with jib71's last post.

For someone who is mostly interested in "old architecture and historic monuments" it is really hard to justify a stay in Tokyo.

NGO can make an inexpensive landing pad for visits to the Kansai region. As well as the Shinkansen (which is certainly the easiest and most convenient option - 5,840yen, 35 minutes, each way) there are several bus companies that will take you to Kyoto cheaply, and the trip only takes 3 hours (including a 20 minute stop), or there's the non-shinkansen trains which will take the same time and cost 2,500yen each way.

I think the itinerary from jib71 is pretty much ideal. You might like to go a little further West and combine this with a visit to Himeji castle and a stay at Hattoji villa.
http://www.harenet.ne.jp/villa/villa/hatto.htm

A night or two in Osaka should sate any cravings for a big city 'hit' (certainly better than Nagoya will). Nagoya station is, I believe, the largest in Japan and is worth exploring in its own right, but I think your comparison of this city with Frankfurt is spot on.

I should stress that I adore Tokyo, but it needs lots of time (and research) dedicated to it. Osaka yields it charms much more quickly (and brashly). The downside is that it also seems to exhaust them sooner, but it should take more than 2-3 days to get to this point. I'm in love with Tokyo, but I still retain my infatuation with Osaka.