Wirelessly posted (Xperia Z: Mozilla/5.0 (Linux; Android 4.4.2; C6903 Build/14.3.A.0.681) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/33.0.1750.166 Mobile Safari/537.36)
I guess one has to ask where exactly op is heading in kyoto. If he is going to kyoto station then it should be JR, however if it's those temple area either one should do fine as you connect to bus anyway. If against the river area and the bridge / sightseeing train then hankyu.