The physical incompatibility of the title is the theme running through this series, but it's not really about that. It's about the Japanese cultural disinclination to discuss delicate matters openly. It's about how Japanese women, in particular, are taught that they should experience a life of depravation and discomfort before they ever deign to bring up something embarrassing. How communication, which is so central to any good marriage, is secondary to cultural norms of subservience and deference.
That's not to say the long silences, and the reluctance of BOTH characters to resolve their physical incompatibility, wasn't aggravating and occasionally infuriating. In this day & age, there are SO MANY options they could have explored -- both to please each other, and to alleviate the wife's discomfort -- but the writers chose not to explore what would be normal, common-sense measures.
I enjoyed the series, even though it occasionally infuriated me, because it gave me such a good insight into a very foreign culture.