Two myths about Japan that are commonly repeated is that it is small and that it is very densely populated. Take a look at the map below. Does Japan look small to you? It is actually about the size of America's eastern seaboard. Note that the latitudes were kept intact in this image.
Japan is physically about the same size and shape as the portion of the US east of the Appalachian mountains. It also has similar weather: Okinawa (Naha on the map) is little different than Key West. Hokkaido, the northern-most island, is like New England with lake effect snows blowing in from the back side. Also note that while the population of Japan is about 128 million, the population of the eastern seaboard is on the order of 80 million, depending on what you count. So while Japan is more population dense than the eastern seaboard, it is not wildly different. The image of Japan being super-crowded is because people choose to live in its cities, particularly on the eastern shore, and country-side sprawl is not as common as it is in the US. If the Japanese were willing to live further inland in the minor cities, their density would not be all that different from what is found in much of the USA.