Currently in Japan, only Ryukyu Islands is separated into a region but not other airports in the country.
To facilitate navigation, and also given scope of operation of real life regional airlines, I think it would make sense if three more regions are to be created in Japan, covering respectively Kyushu, Hokkaido, Izu Islands.
Doing so would make it easier for players operating smaller airlines in each of the regions to locate and access small airfields around them.
Or if only Honshu and Shikoku airports left not classified into regions is not desired, then each of the two can also become regions.
Sounds sensible. I’ll add it to the list for a future data patch.
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I believe the optimal approach would be to divide Japan according to the regional classifications that are commonly used within the country: Hokkaido, Tohoku, Kanto, Chubu, Kinki (Kansai), Chugoku, Shikoku, and Kyushu (with further consideration on whether to include or separate the Ryukyu Islands).
Japan has around 75 airports with scheduled flights, which is a high number compared to countries of similar or larger area such as France (about 50 airports), Germany (about 35 airports), and Italy (about 40 airports).
Therefore, dividing the country into 7–8 regions should not be a problem and I believe it would help improve usability.
Generally, I like to use the subdivisions as defined per ISO 3166-2, but for Japan those are the 47 prefectures, which is too much.
Wikipedia lists 8 “regions”, which sound like what you have in mind: List of regions of Japan - Wikipedia
Personally, I’m happy with whatever feels right from a local’s perspective 
I find it frustrating and time-consuming to search for airports by breaking a country into regions. I would prefer removing that structure entirely and instead listing all airports in a country together, with the region shown as a separate column in the table.
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Those are indeed typical regions of Japan but which prefectures belongs to which region could varies in different settings. Niigata, Nagano, Yamanashi, and Shizuoka are classified as Chubu in the wikipedia article, but because they belongs to East Japan Civil Aviation Bureau for the purpose of airport and air route management, grouping them together with Kanto as Kanto Koshin Seietsu could be better.
Alternative option is to just use Honshu to cover the entire Honshu island, which is not that typical way of classifying regions in Japan but it can avoid the problem of where region boundaries are and the entire Honshu do not have that many airports in total anyway, so I think it is a possible alternative solution
Disclaimer I would not say I am local of Japan despite my personal knowledge and experience in the country.
yh I will say Ive found this dilemma, if your very familiar with a country then it generally makes navigation easier but if your not then it can be a bit of a lets see whats behind door B type exercise.
For the most part its not too noticeable as often you have a good idea of where you want to fly so u can just search up via ur icao or iata codes whichever your prefer. But on some rare occasions you might find yourself like I have where ur looking through countries out of curiosity in case you want to try out a new route. This is where u run into that qol issue uve described, while I dont mind browsing around a bit. It might be worth having it be considered if we get a future ui redesign?
Also when I’m going through regions I open each one on a new tab so it can just be closed & makes getting lost less likely. Its a solution that helps me anyway so figured its worth a mention 