When comparing Nagasaki vs Ishigaki Island, the Slant community recommends Nagasaki for most people. In the question“What are the best cities to visit in Japan besides Tokyo and Kyoto?” Nagasaki is ranked 7th while Ishigaki Island is ranked 9th.
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Pros
Pro Atomic bomb memorial
Pro Castella sponge cakes
When the Polish first came to Japan through Nagasaki's ports, they brought with them their egg-based sponge cakes. 400 years later, Nagasaki has really refined their recipes, and this cake is one of the favorite desserts of Japan. Some of the historical shops still operate their flagships in Nagasaki, where the cake is exquisite and service and impeccable (change is doled out in completely new bills with consecutive numerical codes).
Pro Beautiful night-view
Nagasaki was rated as one of the best night views in all of Japan. Given its unique coastal structure, there are several great viewpoints around the city.
Pro Unique culture and history
Since Okinawa was originally a separate country from Japan, Ishigaki is one of the best ways to explore Okinawan culture. There are unique food, phrases, and styles of dress visible all over the island.
Pro 'Hawaii' of Japan
The second-largest island in Okinawa, there are long strips of beaches all around the island.
Cons
Con Underdeveloped public transportation system
Con Need a car to get around
While there is a bus and some taxis, the more efficient way to get around is by car. Renting a car will mean added costs, but it offers the most freedom to fully explore the island.