Pack for the region and the month, not for Japan. Here is the whole year, plainly.
Japan is long enough that a single national forecast means little, but the pattern holds almost everywhere: a mild dry spring, a green June, a clear dry autumn and a cold dry winter — with snow on the Japan Sea side and sunshine on the Pacific side.
If you can choose your month, choose late October to early December, or late March to May. Those are the two windows when the weather is comfortable and the country looks its best.
Two things surprise people. June is not a washout — it rains in bursts rather than all day, and the gardens are at their best. And Hokkaido has no rainy season at all, which makes June an excellent month to be in the north.
August is the Japanese holiday month — expensive and busy. It is a good month for Hokkaido and the mountains.
Golden Week (late April to early May) and New Year are when Japan travels. Transport and hotels fill and prices rise. Beautiful, and to be planned around.
Ask your hotel front desk; they will know what is running and what is not.