Kyoto is an amazing place!
It was the capital of Japan until 130 years ago and is full of incredible temples, shrines and stuff.
I like the atmosphere in Kyoto too, for a pretty big city it doesn't feel so full on as the others.
Maybe it is because it is surrounded by the mountains and the lake.
Ryoanji temple is amazing and so is Enrakuji up on Mt Hiei.
Springtime the Cherry Blossoms are amazing in Kyoto and in Fall the colors are breathtaking.. reds, oranges,golds and yellows.
(Does get a bit busy in Fall, though!)
I think if someone had to choose just one city in Japan to visit, Kyoto would be a great choice!