The Game completely rejects what the First one stood for and with use of a lot of liberty they paint the characters from the first game as complete genocidal evil while the twisted shady cult from the first one is now deemed as people who are hurt and righteous.
That is just the story, the game lacks a direction and vision. They introduce a conflict out of nowhere and the the resolution to the conflict is revenge. And you go on this murderous killing spree which the Writers force you to, and then they force you to sympathize with the Antagonist by pushing the entire Game back to the first day and showing why the Antagonist was right.
What could have been two seperate games is being sandwiched into one and there is absolutely no sense of accomplishment from either sides of the story.