Would you care to read a short literary analysis? Damn. You did ask for it.
Where Fool Moon most obviously fails is in the characterizations of the main characters. Who even is Harry Dresden at this point? The book seems unsure. He waffles back and forth from being patriarchal and clueless. He can't be both, or at least within the rules of this narrative he shouldn't be. Kim Delaney dies because he failed. He still insists he's in charge. And this early in the series, it isn't earned. Even Harry knows it.
It's Murphy's characterization as well. Is she an incredibly canny and professional cop...or not? The book can't make up its mind. She knocks Harry down when he's handcuffed and not resisting, chipping his tooth, and its incredibly out of place even for her characterization so far. Later, she shoots the loup garou over Harry's ear, and this was not earned by the narrative. Why did she suddenly trust him right then? It feels like Butcher was unsure of how they would relate to each other long-term, and so he left both paths open...at the expense of being decisive in this book's narrative. It's cool if you're a fan and know the whole canon, but reading Fool Moon as the second book in a series could easily leave a reader confused.
Fool Moon has Harry acting like a patriarchal asshole that he really isn't, and Murphy acting as a shoot-first-ask-questions-later cop that she also isn't. It's even obvious when comparing both of them to Storm Front, the only book that came out before it. They both feel like different characters. It falls apart.
To delve into the narrative, Fool Moon leans on Marcone heavily. And Marcone shouldn't be the main antagonist. Based on every indication the narrative gives, Finn, the Loup garou, should be. But he never is. By night he is a murderous beast, yet we're meant to side with him over Marcone, who the narrative has given us no reason to hate outside of Harry's exposition...which even by now the reader has been trained to not always trust.
Fool Moon also introduces FOUR TYPES OF WEREWOLVES into what is, at this point, a basically brand new canon. It becomes hard to follow because of that convolution. That's just too many types of werewolves. And I actually think Butcher does a great job keeping all the werewolf types distinct from one another, but that cuts into the pages he can use to build Harry and Murphy. That's part of why it suffered in my previous paragraph. Four types of werewolves that must be explained is a problem in a book this size. The narrative just can't fit it, while also doing justice to its crucial characters. I have come to love Fool Moon as part of the lore when considering the series as a whole, but as a ~250 page novel on its own? Oof. Butcher makes it work, because he's amazing...but it's clumsy compared to his other works.
If you press me, I could come up with more stumbles in Fool Moon's narrative. But I've already talked your ear off. I'll let it go now.
I'd like to reiterate in this paragraph that I LOVE the Dresden Files. It is perhaps my favorite series of books ever. And I don't think Fool Moon is a bad book by any means. It's decent. It's a really fun read, even. But it's not on par with almost every other book in the series.