When comparing Yakushima Island vs Ise, the Slant community recommends Yakushima Island for most people. In the question“What are the best cities to visit in Japan besides Tokyo and Kyoto?” Yakushima Island is ranked 5th while Ise is ranked 6th.
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Pros
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 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.