I’d look at going out away from the big cities to ride. Can waste half a day negotiating the bike paths and roads getting into them.
However having ridden into and out of Kyoto it’s not bad. I’ve ridden up the Eastern shore of biwa heading to the Alps it was ok, but from memory south of Kyoto towards Kobe was much nicer but hillier.
Me and my partner did a ride around the Noto peninsula on Blakey’s recommendation. Was very good. Some days were only 35kms, and only two significant climbs.
Another good spot to consider is Shikoku, great riding around the coast and more chill than mainland Japan I found.