Been to Japan in December, August, and May. Plan to go this June. It depends where you are going, but you really should go to Kyoto and the best time is in the spring for Kyoto, April or May before it gets too hot and the flowers are in full bloom. September or October work as well. In May there tends to be a lot of school trips to Kyoto, so you might see large groups of Japanese junior high kids in uniform. We were approached by a few groups so they could practice English.

When we went in December, we went south to Nagasaki and Okinawa for warmer weather. Kyoto was not freezing, but the gardens were bare.

We were this April (13 - 25). . The weather was very pleasant, 22 - 25 Deg. C during the day, sunny. We were very, very lucky to see the cherry blossom in all the places (Tokyo, Kyoto, Osaka). . It was incredible beautiful.
There are some internet sites telling when is suppose to be cherry blossom each year. We could not go then, so we went two weeks later, but, it seaams that what they anticipated in internet was not very accurate, because this year the sprimg was later, and we were lucky.
Any case, Japan is beautiful in sspring aand the weather is perfect for trips.