The main issue is the separation of the story into character and plot elements. It is fairly indisputable that the game choses to focus more on the character development than the overarching story of the events. To someone who is primarily interested in the events of the game it will appear to have a much weaker plot than to one who gives more credence to the character aspects.

With that said, many (including myself), feel that the plot was written to serve the character development and not strong enough or developed enough to carry the game on it's own. After the character development is effectively concluded mid way through chapter 9 there appears to be very little effort put into making the game's story engaging.