When comparing Nagasaki vs Ise, the Slant community recommends Ise for most people. In the question“What are the best cities to visit in Japan besides Tokyo and Kyoto?” Ise is ranked 6th while Nagasaki is ranked 7th. The most important reason people chose Ise is:
The Ise Grand Shrine is unique in Japan as being the top of the hierarchy of Shinto shrines connecting to Japan's imperial house. It is taken down and completely rebuilt every 20 years.
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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 Home of the highest ranking Shinto shrine
The Ise Grand Shrine is unique in Japan as being the top of the hierarchy of Shinto shrines connecting to Japan's imperial house. It is taken down and completely rebuilt every 20 years.
Pro Ise lobster
Despite being a small town, Ise is home to the Ise lobster, which is well-known throughout Japan for its culinary applications. There are entire traditional course meals using the Ise lobster at Ise's traditional inns.
Cons
Con Underdeveloped public transportation system
Con Not a lot to do after a few days
Ise is a small town, so there's a fairly finite number of attractions in Ise. Ise is best for 2-day-1-night trips.
Con No direct bullet train to Ise
If traveling from Tokyo, travelers must transfer from Nagoya onto the local rail system to get to Ise.