All roads lead to Kyoto, at least that's what most tourist brochures and travel documentaries on Japan let you assume. The ancient capital does indeed lie at the heart of the Kansai region but it would be a shame to restrict your travel solely to the well-beaten track. Japan's even more ancient capital, Nara, is less than an hour away by rail and it's easily worth staying a night or two there. Further south, the landscape becomes more rural, the crowds thin out and the views are worth seeking out. Kansai has one of the most extensive networks of rail lines in the country (operated by JR and private railways), which means you can go off the beaten track without the fear of leaving the big city far behind.
The first part of this route guide follows the shinkansen line from Nagoya to Osaka via Kyoto - there is relatively little to see en route but it's useful if you're in a hurry. With more time, consider a much longer route to Kyoto via the rural Kii Peninsula, easily accessed from Nagoya but very much off the traditional tourist trail. Limited expresses operate around the peninsula so the journey needn't be too time-consuming; the countryside and coastline certainly repay the effort. Taking this longer route also gives you the opportunity to go to Ise, home of the Grand Shrine and spiritual centre of Japan's indigenous religion, Shinto.
Finally, another spiritual centre, the mountain retreat of Koya-san offers a wholly unexpected change of pace. Koya-san can be accessed from Kyoto, Nara or Osaka, or as part of a longer journey around the Kii Peninsula and is ultimately reached by a hair-raising cable car.
If you've arrived in Japan without a rail pass, JR West, which operates services throughout the Kansai area, sells regional passes over the counter.