Onomichi has lots of locals living in it, but it's definitely a popular place for Japanese locals to visit. From that perspective, it's still interesting for a foreigner, but has some of the same drawbacks as the standard touristy cities.
Miyajima is a popular day-trip location from tourists in Hiroshima, so there's quite a few people walking around town during the day. However, the last boat back to Hiroshima leaves prior to sunset, so watching the famous tori gate during the sunset will be far less crowded.
Since Kanazawa is a popular destination for Japanese people, and foreigners tend to go to Kyoto, many of the attractions in Kanazawa are less language-friendly to English-speakers. That being side, most signs are in English, and many of the main attractions still offer pamphlets and directions in...
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.
Kasuga Shrine is one of the oldest shrines in Japan and the head of the Kasuga branch of shrines. The moss covering much of the architecture is unique compared to the spotless shrines in other parts of Japan.
The annual festival in February showcases hundreds of ice/snow sculptures. Some as small as a life-size pikachu, others are full-size illuminated light-show castles. Along with all the sculptures are music, food, and game events.
Aomori ships the majority of the apples that get consumed around Japan, including the expensive $10+ per apple gifts that get presented in special occasions. Thus, Aomori is the prime location to try these apples at a more affordable price.
There are a lot of famous foods in Hakata: motsu nabe, tonkotsu ramen, mentaiko. While there's also a few shrines and gardens, Hakata is a fairly modern city and thus doesn't have a lot of traditional cultural attractions.
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.