A few notes about things I do when I travel to Japan.
I travel with a carry-onable back pack. Anything larger would be obnoxious when negotiating trains/bus stations. Specifically, I travel with an Osprey Porter 46. Even with that, I usually plan my day around dropping it off as quickly as possible (even if it's prior to check-in, hotels will always hold it for you). If you ever need to ditch your bag, search any major train station for coin lockers large enough to cram it in (coin lockers are typically deceptively deep and spacious).