Very clean.

Most have both types of toilets available. If not, go to the handicap toilet, it is always sit down type.

Having lived in many countries, China and Taiwan included. Japan's washrooms are a godsend and impeccable. Japan's worst washroom is still pretty good in comparison to some of the "washrooms" (try hole in the ground, no stall doors) I've had to use.

Most today have toilet paper however I have noticed that outdoor lavatories do not necessarily have toilet paper available so bring your own if you are going to use remote toilets.

All convenience stores, department stores, government buildings, hotels, gas stations have great bathrooms.