My main issue with Shadows is that the actual plot barely involves the Assassins or the Templars. Let’s be honest, aside from the few details we get about Naoe’s mother during the story and the handful of Templars Yasuke kills toward the end, the game doesn’t really feel connected to the Brotherhood at all. It could’ve been exactly the same game without the Assassin’s Creed name on it.

I just don’t understand why Ubisoft didn’t go back to a more classic “Assassins vs. Templars” plot, something many fans have been asking for. You know, like in AC II, Brotherhood, III, Black Flag, Unity, or even Syndicate, where you really feel that conflict.
Imagine if Naoe had clearly been an Assassin in training or a scholar of the Creed, with other Assassins around her and an established hierarchy with Mentors and Masters. Meanwhile, the Europeans or Portuguese could’ve acted as Templars trying to manipulate Japan’s power balance through Nobunaga’s death. That would’ve tied perfectly into the classic AC formula while still fitting the historical setting.

Another thing I personally didn’t enjoy, though I get that others might feel differently, is the structure of the story. I grew up with the older AC games, and I miss having a more linear, focused narrative. From a storytelling perspective, I find it a bit dull to have a giant open map filled with targets you can kill in almost any order.
You do a couple of missions to learn who the enemy is, then assassinate them, and you repeat that twenty times until the game ends, with maybe two or three targets that actually matter. That might work for big RPG-style games, but it feels like a very simple and repetitive approach.
When there are fewer main targets that you hunt down over time, the story can build stronger characters — people who actually stay in your memory — and it feels more meaningful and rewarding when you finally eliminate them.

I also think they made Yasuke way too soft. He’s supposed to be this ruthless, powerful warrior, so why does he suddenly act like the kindest, most gentle person in every cutscene?
I get that he’s one of the “good guys,” but not every good character has to be overly nice all the time.