The Best Season in Kyoto is Winter.
After I was born in Kyoto, I have had four seasons of Kyoto many times. Every season has special character and it's so beautiful, but among them, the best is Winter, I believe.
As you know, Kyoto is extremely cold in winter, but wonderful. I think that real beauty exists in silence.
When I was a kid, I frequently went to upstream of Kamo River with my farther to give some bread to Yurikamome, white migratory birds from Siberia. It's cold enough to hurt my ears, but that was a seasonal fun to play with them until they leave for a long journey ahead.
Kyoto is not just sightseeing of temples and shrines. It's full of nature.