These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Magnificent Bastard — Kaede for much of Grass For His Pillow, Muto Kenji for the whole series. Arai wishes he was this, but ultimate gets killed at the Manipulative level.
Mind Game Ship — Possibly the best way to describe the complicated relationship between Kaede and Fujiwara; it's debatable whether it can be called a "ship" since they are explicitly not interested in each other sexually, but he is fascinated in a rather intense way by her secrets and mystery, and she finds herself responding in some way to such focussed interest from a man who desires more than simply her body. She herself is not sure what part of her is responding and what it is responding to, but she definitely has some sort of reaction to him. She ultimately shares her secrets with him, and though she does it for pragmatic reasons, she finds a strange sort of intimacy with him despite the fact that he repels and frightens her just as much as he attracts and fascinates her. They ultimately marry, though it was forced on Kaede's part, and once he "possesses" her in this way, he loses much of his interest in her. However, even in the last book, Takeo is made uncomfortable when he is reminded of the connection, because he's aware that Kaede's relationship with Fujiwara was very difficult to pin down, and was in some ways just as intimate as her relationship with him.
Moral Event Horizon — The Tribe have a lot of Gray and Gray Morality, and though they don't always agree, they tolerate each other for the sake of keeping the Tribe together. However, Kikuta Kotaro manipulating Yuki (Kenji's daughter,) into bearing Takeo's child and then having her murdered by Akio is considered completely unforgivable by many prominent Tribe members, and the final separation of the "good" Tribe members from the "bad" is decided by what side they take after this line is crossed.
Earlier, Takeo considers Kenji to have crossed this when he helps to abduct him before he can kill Iida, thus ensuring Shigeru's death. However, he later reconciles with him after gaining a better understanding of the Gray and Gray Morality and total loyalty to the Tribe that all members are conditioned into.