Rain is a planning signal
Rain does not ruin Japan, but it exposes routes with no margin. Mark which days need good weather, which tolerate light rain and which are true backups.
Cities handle rain better
Tokyo and Osaka usually absorb rain better than Kyoto, Hakone, Fuji or coastal day trips because they have more indoor options and shorter exits.
Kyoto needs care
Rainy Kyoto can be beautiful, but long outdoor days with buses, slopes and crowds can become heavy. Choose fewer areas and stronger lunch anchors.
Keep flexibility
Do not hard-book every weather-sensitive experience. Use current updates before locking the final week.