Japan is not relatively a small country and is consolidated with many large & small islands (surprisingly more than 6,000) all over the country.
Japan is consisted of 4 major parts, which are "Hokkaido", "Honshu", "Shikoku" and "Kyushu". Japan has total 47 different prefectures locating from northen Japan to southern Japan.
a) Many people know about "Hokkaido" which is well famous for winter weather, snow scenary, fresh seafood, sightseeing spots in the northen part of Japan
b) Honshu is the largest part of Japan, which is named as a "mainland" to cover the majority of its population and industries, including many big cities such as Tokyo, Osaka, Nagoya, Kyoto, Yokohama, Kobe and others.
c) Shikoku is structured with just four preferectures that are having abundant aguriculture, fishery and natural resources.
d) Kyushu is located in the south-western part of Japan, which is closer to China & Korea. In the history Kyushu ever had important roles to communicate and trade with foreign countries, particularly in Nagasaki, Hakata, Kagoshima and others.
Having said, there are so many nice & attractive places to visit and see in Japan. I believe you definitely like to try out Japanese authentic & traditional cuisines such as "Kaiseki", "Sashimi", "Sushi", "Tempura", "Wagyu-Beef Shabu-Shabu" / "Sukiyaki", "Yakitori", "Tofu Delicacy", "Japanese Soba" / "Udon" and absolutely "Original Japanese Ramen". Furthermore, I also believe that you like to go and see wonderful "Mt. Fuji", "Cherry Blossoms", "Autumn-Leaves", "Winter scenaries" as well as experience yourselves in "Onsen" (Hot-Spring Bath) with Japanese "Sake". Really, so many things and places there! That's why your good planning is so imporant and necessary to make up your holiday so satisfied.