Their mistake was getting a separate team of writers to make the expansions of AC2. This separate team is the reason we're in this mess because they ruined the character of Desmond.
Originally he was supposed to be a representation of you. In AC1, you learn everything as Desmond learns it. And with the story, they made it so that you can basically insert yourself into his position.
But the AC2 expansions completely obliterated this character by giving him a backstory and more of a personality. They made it so the Desmond of AC1 is no longer you, and is actually a very vague, boring, flat, uninteresting character who's motives are nonsensical.
Long story short, the ACTUAL writers of Assassin's Creed had to fix the gargantuan problem caused by the expansion team and they did this simply by killing off Desmond. Given the situation they were in, I would say they made the best story they could have in AC3 given all the plotholes.
So I'll be getting AC4 if the real AC writers are behind it.
Also I want a female assassin :3