I have bad memory of beating the game, but what exactly is the relationship between Ujiyasu and Kai? I was certain that when you beat the nation in the main story, Kai calls Ujiyasu "dad", but when I look at the info in Samurai Warriors, she's simply the retainer. Maybe I got it mixed up and assumed Kai meant dad if she called Ujiyasu "old man" (because she does do that in Samurai Warriors with a slip of the tongue.
From what I understand, they were changed to being parent and child in this game because, in the original franchise, Kai simply has a crush on Ujiyasu, and they didn't want to freak people out with that big of an age difference so they made it more family-friendly for this game.
I thought they were Uncle and Niece?
When you evolve Ujiyasu, his warrior skill becomes "Father-Figure". That could contribute to some confusion as well.
Why aren't Kyogre and Kyurem in the game? It'd be one thing if only one member of the trios they belonged to was in the gamenote The Weather Trio and The Tao Trio, respectively, but it seems odd to have 2/3rds of each of their respective trios in the gamenote Groudon and Rayquaza/Reshiram and Zekrom, respectively. While it's true that it would be impossible to give a legendary Pokemon to every Warlordnote both at the time the game came out and as of Gen VI, there are no poison type legendary Pokemon, excluding Arceus holding a Toxic Plate, meaning that even if every other Warlord received one, Nene would be left out, it seems like it wouldn't have been THAT hard to include 1-2 more legendary Pokemon in the game. Also, as noted in the YMMV section, it would've been a better fit thematically for Mitsuhide's legendary to be Kyurem instead of Arcticuno. And while it's true that Rayquaza could stop Groudon if it went on a rampage, Rayquaza only appears in cases where BOTH Groudon and Kyogre's abilities are out of control - no Kyogre, no Rayquaza!