From about 1641-1853 the Tokugawa shogunate enforced an isolation law that was made to keep outside people's and industrialization out of japan and from threatening Japan's livelihood at the time.
Because of this long period of isolation in most parts of Japan, Nagasaki was inhabited with lots of worldly growth. Settlers, explorers, missionaries, and scholars came from all over the world to learn of Japan's culture, and to spread knowledge of their own. Most notably the Portuguese and Dutch had a large influence on Japan at this time because of their medicinal/industrial knowledge but also the Portuguese's brought Christianity to Japan as well during this time.
The atomic bomb that the USA targeted Nagasaki with was purposeful in destroying such a historical city of Japan. The devastation of the 1945 "fat man" atomic bomb can still been seen thought the city today. The atomic bomb museum dedicated to preserving the memory and the people who lost their lives to the bomb and its after affects is located exactly where the bomb originally hit.
Nagasaki is an amazing city with an extremely cultured past and present. This city was home to the emperor at one time, was the only port in japan open for 200 hundred years to the rest of the world, and was victim to second and last atomic bomb to ever be bombed for real. For these reasons I believe Nagasaki to be the most historically important city in Japan.
