I wonder. If there WAS a poll that went up and the vast majority voted that they liked the story overall, would that cause a number of these people who shout about the poor story to suddenly become silent?
Well, we're not all shouting or calling for Chris Metzen's head. ;)
In my own opinion, it's not the story that's flawed, it's the delivery. Most of us had guessed that Deckard Cain would breathe his digital last during the D3 storyline, but a lot of us were shocked at how callously this was handled. We didn't expect him to go down fighting while defending Leah/Tristram/his book collection against a horde of ravening hellspawn, but to have him murdered by a poorly conceived minor villain is just...wrong. At least have him slip away peacefully after whispering some vital clue to those gathered around his deathbed.
And Tyrael. Unlike others I think his choice to abandon his heavenly powers was awesome and awesomely portrayed...in the cinematic. Then he got into the game and immediately became "eat up with the dumbass", as the locals here like to say. Even as a recently retired angel, shouldn't he have guessed at Adria's true motivations, Leah's true heritage? Shouldn't he have been warning the player? There's a difference between suspending your disbelief and throwing it out the window.
That's just two examples I can think of off the top of my head. I'm sure there are others.