The last reason is more of a personal opinion, but I did not enjoy the story. Or, more precisely, Aya's role in the story. The story itself begins similar to Ezio's story, with murder of family and the thirst for revenge that follows. Unfortunately, by the point you meet Aya for the first time, she, to me at least, does not seem to follow that path, but rather tries to follow this greater purpose scenario (or Ezio's later story).
In the end, there is but one situation I can recall where she shows a want for revenge (other than congratulating Bayek after a plot kill), and this is at the end of the game when all has crumbled around her. This created a feeling of disconnect. She was not fighting for the same reasons I did (or so it felt at least), making me less inclined to like her.
So when the end came, I felt both cheated out of Bayek's last kill and annoyed at the importance she was suddenly given (and by that I do not mean she had no importance before, but, before the end, she was merely another story NPC to me, albeit one with some annoying sailing missions).
All in all it felt like they took Ezio's growth during his story and divided it over two characters creating a disjointed experience (in the way that I was not sure whose story it was meant to be) where it felt that Aya started the Brotherhood using the goodwill Bayek accrued over the course of the game. Especially because we (or I at least) know very little of what Aya is doing during the game which made me feel like she used Bayek's accomplishments to bolster her own goals while doing not much of note herself.