ksandness

I don't know. The train system in Japan is so good that I've been tempted to fly domestically only once, and that was due to a special package deal for traveling to Kyushu forty years ago when I was studying in Japan.
Here are the advantages of taking the Shinkansen between Kyoto and Tokyo:
You can get up and move around, and there is plenty of leg room, even for a tall Westerner like me.
You can see the countryside and get a glimpse of some of the smaller cities, including a good long look at Mt. Fuji from the north side of the train, as long as you're traveling in the winter.
There are no airport hassles--the Shinkansen goes from Kyoto Station to Tokyo Station, without worries about how to get to and from either airport, no security lines. Two hours, fifteen minutes, central city to central city is hard to beat!
Buy the ekiben (train station box lunch) of your choice, and eat it at leisure, supplemented by beverages from the station vending machines/kiosks.
Why take yet another plane ride when you will be facing two long plane rides at either end of your journey?

By the way, you have two options for Kyoto to Nara, as long as you're not buying a JR Pass: the JR option, which lands you in one part of town, and the Kintetsu (private line) option, which lands you in another. Both leave from Kyoto Station. The main attractions in Nara are pretty close together in a park-like setting, but the Kintetsu option brings you slightly closer to them, and is usually slightly cheaper.