I landed in Osaka and I took off from Tokyo, but you can land and take off in the same airport and take the shinkansen (2h30). For example you land in Tokyo, you do the itinerary reverse, you arrive in Kyoto and you take the shinkansen from Kyoto to Tokyo on the last day.
Anyway, I landed in Osaka, I rented a car directly at the airport (with times, very reliable rental car company) and I went to Kyoto directly. If you want to spend some time in Osaka, check my other itinerary.
I landed at 8am so I had the whole day ahead of me, left the airport around 10am, so I had many stops on the way before Kyoto.
Yokoku-ji dani KANNON
Komyo-ji
Bamboo Path (Take-no-michi)
Saihōji (Kokedera) Temple
Arashiyama Park Observation Deck
Kitayama Big Daisugi
Genko-an
I booked 2 nights in The Prince Kyoto Takaragaike. It's a bit outside Kyoto city center, but if you have a car, it's very nice play to stay.