Tokyo has its share of shrines and historic sites, and many others are within day-trip distance (Kamakura, Nikko, Hakone, Kawagoe and Yokohama to name a few). The cities in the Kansai area are large, but tend to have a slower pace than Tokyo...actually any other city will have a slower pace than Tokyo.
I wouldn't hesitate to call Tokyo a concrete jungle, but there are spots of natural beauty that can be seen even within its borders. Travel a few hours to the southwest and you can reach the Izu peninsula and visit areas like Atami that have some pretty nice onsen.
I'm partial to Tokyo because that's where I spent the majority of my time, but clearly biases are common here, for various reasons