There is no geepney and tricycle in Japan. Alternative transportation is train, route bus, and taxi. Needless to say, taxi fares are higher than trains and buses. Incidentally, Japanese taxi has a automaticaly door.
Perhaps if you will live in Japan, you need to walk longer than in the Philippines. Because trains and buses have routes and places for getting on and off.
By the way, there are substantial trains and bus networks at near urban areas, but it is not in the countryside. If you consider to live in the countryside in the future, please check the necessary transportation. You may need to depend on someone’s driving.