You can't really compare Japan to all of Europe. There are major differences in Europe on all of your points. As a German that lived 6 months between Osaka and Kyoto I mostly agree on the last one, but cleanliness and public transport is only slightly behind so that it doesn't really matter. E.g. Japanese streets are astonishingly clean, but I have never been disturbed by litter in Munich. Garbage doesn't pile up here. Also the public transport works really well, mostly in 5 minutes intervals in peak hours and 10 otherwise. The "Stammstrecke" in the center is also served in 1-3 minute intervals.