All seasons have their strong points in Japan. Autums is great for the colored leaf and all the events surounding it. Winter can offer stunning landscapes, and there is nice events in colder places where they have snow, there is also many new year ritual that are worth it and illumination. Spring is fantastic for Plum Blossom and for Sakura. Summer is hot, but there is so many festival and activities.
I would say that my favorite is spring, as I live in a cold country, there is no plum an cherry trees that bloom like in Japan, especially not in the city.
And the worst is taifu season.
For a tourist, fall is definitely the best season. The temperatures are mild, the autumn colors are gorgeous, and there is so much to see and do. Spring is similar, but there is a lot of rain during the transition from winter. Winter is only the best choice if you enjoy skiing and other snow-based sports (or if you want snow-covered photos). Summer is definitely Japan's worst season - unless you are traveling around Hokkaido or if you are a serious 'beach' person.
I've learned to appreciate all of the seasons here (though summer takes a LOT of effort ...) but autumn will always be my favorite. The vibrant display of the maples and ginkgo trees, the cooler temperatures, the reaping of the rice, the transitioning of the menus to heartier, warming dishes ... it never gets old.
I actually like the uniqueness of what each season brings, to put it simply, I love all the seasons in Japan. In winter, it is cold and some parts of the mainland Japan gets enough snow for a perfect all-white scenery, yet not as terrible as the snow in Canada and other 4-season countries. In summer, everything looks vibrant and green and the weather is hot, but not as hot as the summer in China (it was terrible due to too much pollution). Spring also gives a great picture of the cherry blossoms. Other countries have spring too, but they do not have as much sakura trees as Japan, and autumn, the picture perfect reddish, orangey and purpish views of the mountains makes the surroundings beautiful. So, it's hard to pick only one season because each season has its own beauty when you capture it in pictures, particularly the seasons in this beautiful country.