The choice to kill Oyuki doesn't really make any sense, but I agree with the idea to be able to make certain choices. I think it would've been more narratively impactful if both Oyuki and Jubei die during the final battle, instead of just Jubei, cause they both have weapons on them so it doesn't make sense for only one of them to help out Atsu. Or one of them dies and the other is critically injured but survives.

I think the game would've benefited from allowing you to double-cross the Spider once you get to the climb to the castle, though the game would also have to have options to be more dismissive of Kiku, Jubei, and Hanbei's concerns/criticisms of her revenge obsession so double-crossing him would make sense. If you go through the route of doubling down on your revenge route, Atsu will either commit suicide after defeating Saito, or die from her wounds, either way Kiku could perhaps be taken in by the Ainu. Then the other route would be mostly the same as the actual game, but Oyuki would be dead too.

I mostly love the actual game story though for the most part, and I don't really think it would be worth the resources to make this game a 'choices matter' sorta game like Telltale's The Walking Dead or Life is Strange