We spent in Kyoto three nights and almost four days, and I really suggest you to do the same, as there is so much to see and do in this amazing city – for many the true symbol of Japan's history and culture.
The city itself is not that big, and it's very easy to tour thanks also to the wonderful network of busses (plus the metro) that we happily used to go quickly from a place to the other. The problem is in fact, that there are so many temples and gardens that are worthy to visit, but they are all scattered across the town. For this reason, I decided to separate the central and eastern part from the western part and Arashiyama, which is another popular destination.
The Kamo-gawa river - and its parallel canals - that runs north to south is also a good point for orientation, as most of the temples of the eastern side (Higashiyama and Gion) are on the right of that. The street grid system is also very convenient for touring Kyoto, with its main arteries of Gojodori, Shichodori and Oikedori (parallel) and Kawaramachidori and Karasumadori (perpendicolar).
You will most certainly arrive at the beautiful Kyoto station, which is surrounded by modern buildings and shops and lays pretty much at the center of the city.
We decided to stay in the more quiet part of the town of Shimogyo Ward, between the river and a canal, and half-way from the Kyoto station and the major temples of Higashiyama. The newly-renovated Hazuki Inn is a small but lovely ryokan managed by the very kind Takase-san. Right next to it there is also a small family-owned restaurant where we had a delicious dinner the last night.