Ryokan in Kyoto is a must. Also, if you spend enough time - don't just do Shinkansen all the time. It gets boring pretty quick as you are moving from one big city to another. Rent a car for some time too!
The Japan Rail Pass for those on tourist visas/entry stamps is a sweet deal that I take advantage of whenever I travel to Japan and visit different regions. It allows you virtually unlimited access to the Shinkansen and other routes operated by the various Japan Railways companies (such as Tokyo's Yamanote Line and the Narita Express) for 7, 14, or 21 days, beginning on the date that the pass is activated. I say "virtually unlimited" because there are some restrictions, such as not being able to take the fastest version of the Shinkansen that has limited stops between Tokyo and Osaka; instead you're restricted to the Shinkansen schedules that make more stops (it's still very fast even when stopping at every Shinkansen station, though). I don't know what the prices are like today (it's been five years since the last time I purchased a Japan Rail Pass), but in the past the cost of the seven-day pass was comparable to the round-trip Shinkansen fare between Tokyo and Osaka. It was a fantastic deal for somebody traveling often between different regions of Japan.
Nothing wrong with the normal train lines though.