The Animus plot was okay in the beginning, and it was even somewhat interesting in AC Brotherhood — you got to do something in the "present". But then, they borked the end of the plot; it was never interesting afterwards.
I can understand the author of the article dropping the original title in the middle out of boredom; it was more a proof of concept than a finalized game. However, I found AC 2 breathtakingly beautiful, with a much more interesting story. I haven't played games after Syndicate, but most of those I played gave a really deep immersion in historical events, full of explanations about what was going on at the time, with the odd details — e.g when Robespierre was arrested, he was found with a gunshot wound to the jaw; probably a suicide attempt but details aren't known. Well, that's a scene in the game.