People do care about the story. Just because it's confusing for you doesn't mean it's confusing for everyone. I commend the series for not shoving retcons into Desmonds story. If you read all the documents in AC 1 you can tell what Desmonds story is going to be about and how it's leading somewhere.
I like all the past stories, they serve as the main gameplay, additional story and character additions, and they serve a way for Desmond to learn how to be an Assassin. I never got why people think a non linear story is automatically bad. By the same token I never understood why people think non linear stories are automatically good either. This story just strikes my fancy really. I am all for good gameply but for me if I don't like the story I would not be getting these games on release day.
But as far as overall elements go I'd say this is about the same as Brotherhood in terms of quality. I think AC 2 was my favorite overall because of it's long and compelling story. AC 1 still sticks out in my mind as being the weakest with the repetition, amount of collectibles, and very clunky combat. But as a whole I feel the Assassin's Creed series is very strong overall, and I think AC 3 will probably be the best by a long shot.
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