Kyoto is the biggest name in Japan. Most of you will visit Kyoto. JR Kyoto station is probably the first step to Kyoto for you. There are so many trains, such as Shinkansen, Limited Express Haruka from Kansai airport, Limited Express Thuderbird to Kanazawa, commute trains to Osaka, Kobe and Nara, Kintetsu train, Kyoto city subway and many many more to depart and arrive in this station.
Nara is the former capital city in Japan and it is older than Kyoto. Many shrines, temples and districts are listed on UNESCO World Heritage, National Heritage and/or National Treasure. When you travel in Kansai region, you may think about visiting or staying in Nara. If you go to Osaka or Kyoto from other cities, such as Tokyo, you can get there by Shinkansen. But when you go to Nara, there are several routes and options. The trip route to Nara is varied by your trip plan and/or the deal which you intend to use.