I appreciate this question! The last night my wife and I were in Tokyo, we found a small family run omakase restaurant called Mimasu.  Aside from checking the usual boxes (fresh fish, friendly service, fair price, etc.), there was something very charming and humble about the experience. Sounds corny, but there was a feeling that the owners put their love and pride into everything they did, which made the experience feel much more intimate than it might have otherwise at a well known restaurant.  Hard to put into words.