Don't worry about finding an American-brand hotel if you're just going to sleep there. Japan isn't some impoverished Third World country with questionable sanitation and safety standards. A Japanese business hotel will provide you with a small but clean room with private bath and maybe a breakfast buffet. What more do you need? Best of all, you can easily spend less than US$100 person a night, especially outside of Tokyo and with the weak yen. I stayed in Hiroshima for only about $65 a night three years ago when the yen was stronger.