I really enjoyed the game itself but yeah, they really botched the writing. It's like there's an actual story there, but you only see the second act of it. The game does mention (quite often actually) that Aiden is a miserable hypocrite and a mass murderer, but it doesn't ever go anywhere with the idea. You spend the whole game waiting for that moment where he turns the corner and realises he's a bad guy, but it never happens. Very weird.
But again, it's a fun game, and I never expected anything from the story portion anyway. I'd still recommend it overall.