Advantages:
The island geography means that Japan was fairly isolated and developed a distinct culture.
The threat of invasion was very less considering the fact that seas surrounding Japan are aggressive in nature.
The volcanic nature of Japanese islands is responsible for extremely fertile soil which makes it an excellent agrarian producer.
Surrounding seas enable a fishing economy to flourish.
The streamlined nature of Japanese islands and the proximity to the ocean ensure that there are no water shortages in the country.
The climate created by the relief, winds, currents etc make it an excellent tourist attraction.
Japan is rich in natural sceneries and the aesthetically pleasing culture adds a flair for tourists to admire.
Disadvantages:
Japanese islands are extremely mountainous and relief makes it harder for development on most of the country's landmass.
Volcanic mountains are common and eruptions can hit at any time.
Earthquakes are extremely common and cities are rebuilt almost every few years.
Winters can get extremely cold and unbearable.