There are 2 sections to this book, a reponse to the 9/11 tragedy and the continuation of the storey begun in the previous volume.
The 9/11 storey is not and never was part of the overall storey and arguabley should not really be included here as such, but on the other hand this is also a collection of the monthly spiderman comics and as such it appears where it does.
For me, the main reason why the 9/11 storey does not work is because of the depiction of well known super-villians being affected in the same way as the heroes and everyone else. Regardless of your fealings on the depiction itself, as a piece of writing it's flawed because it is entirely inconsistant with the characters of the villians themselves, as documented by volume apon volume of tales of them attempting and doing numerous despicable things. Had the villains not been included then I may have felt different about it, certainly Spidey's though processes on approaching the scene and reaction to it felt in keeping with character.
The bit of the book that is part of the original overall storey arc is fabulous and it does not matter how bad you may think the first section is, it cannot be bad enough to cancel out the quality of the second half.