The story's main strength, at least early on, was atmosphere. Putting you inside this city with survivors, factions, and a ever present need for survival.
I overlooked some of the game's early missteps thinking that they were going to be addressed later (I was thinking the game had a good story. NOPE!)
The major issue the game has is that its plot and the atmosphere are antagonistic towards eachother, AND that between the two Plot is far weaker yet is allowed to win out. The second is the game will bend logic over backwards to achieve its plot and atmosphere.
So for example at a certain point of the game you feel like you COMPLETELY graduated away from Rais, he just completely doesn't matter to you anymore. Yet the plot keeps insisting he is your personal archnemesis. He actually went from a dangerously cunning adversary whose stranglehold over the city was felt to a cartoon villain who shoots his allies to prove just how evil he is... In a situation where every single one of his men should be vital (I like to imagine Rais has access to an underground city of henchmen you just never go to)
I'd go as far as to say the overuse of him as a antagonist is one of the large reasons why he just becomes completely irrelevant in the mind of the player. You've cleared his men out like they were nothing. What does he have? More guys? Pft. When early on the fact that his few soldiers were far more threatening then the zombies actually gave them a menace for a tiny bit. Less is more in otherwords.