Hmm, this is turning out interesting. Like, you can see good reasons why the Masaka oppose the Nekuni now, even if there were good reasons for some of the Nekuni previous leadership's heavy handed and borderline dictatorial methods - and more importantly it's palpable that most of the characters have their biases or are not really operating with omniscient perspectives for their feelings on this conflict.
It may sound small, but that you can look at the sides of most of the people directly involved in this battle and see both good arguments and complicated feelings that make either their difficulties or their goals sympathetic, that's good, I think. I don't believe Miyako is going to be as ruthless as her grandfather was, and most of the big things that he used his power to achieve are already buried at this point; but I can see how, now that there's a chance to do something about it on the terms that apply to everyone, Masaka-senpai feels like it's an upheaval that has to be pursued out of principle.
Koichi's slight daftness in regards to his sister's lonely struggle about this isn't even hard to understand; he's been a pariah for years and his sister, despite very different temperament, has aspired to a difficult position both out of being closer to her grandfather in a way, and not wanting to burden her brother, even though those two could never agree - so of course he wouldn't see how exactly it undermines the Twelve Clans's status as a whole rather than merely the absoluteness of the Nekuni, and of course his sister would feel hurt and alienated because she feels like her hard work and her commitment are being discounted so easily, even by Koichi himself. He's realized that now, but that's not going to make everything okay.
I find it all decently complicated, and it makes me more attached to the characters. There are sensible points to the questioning of dictatorship from the Nekuni, especially with so much cropping up, and a lot of well-worn grudges, but there are also complications and consequences that make it a not obvious decision, especially since the person responsible for so much of this infamy is no longer present.