Admittedly, as a fan of The Laundry Files, that's a major problem with the Atrocity Archives, for the first half, anyways. The second half, after Bob and Mo visit the Atrocity Archives themselves, is much better. We meet a variety of Checkov's Guns, several important people, and get a glimpse of the kind of horror that the Laundry Files is all about. The Concrete Jungle, a short story included in the book, is equally absorbing, and sets the scene for all short stories to come, as well as showing us a bit more of Angleton, and giving us introduction to MAGINOT BLUE STARS.
The second novel, The Jennifer Morgue, is very good, and largely free of the problems you mentioned, but is very different from much of the rest of the series, for reasons which will become obvious when you read it. It's in the third book, The Fuller Memorandum, where the series really hits its stride, and gets going.
However, the series doesn't mind an offside wink or two every once in a while, like Persephone's parenthesized Enochian, and the way The Scrum talks about its problems.