The main problem I have with the format is the order. A lot of the time they put them in order by location, even if the plot means that the two first encounters bookend the second half of the book. So you end up with a normal campaign with no sequence breaking that goes:
Encounter 1, 2, 5, 5a, 5c, 4, 3, 5b, 6
Of course, I dont really like premade adventures anyway. Most of the time you have to make up more than half of it on the spot because they didn't expect your players to ask some obvious thing. You can have more than one response per NPC, you know, Mr. Of The Coast.