I just finished reading Artemis Fowl: The Atlantis Complex by Eoin Colfer. I think I'm just going to refer you to this review by Linda Buckley-Archer. As she says, there are many "comic delights" to be had in this book. (Mulch Diggums is close to being my favorite character in this series). But, yes, "electing to have a hero who annoys and a villain who elicits sympathy does run the risk of sapping the narrative energy." And I do have to agree that we're talking "plotting that doesn't entirely satisfy." But without a doubt the book is filled with "humour and brilliant inventiveness."
As far as the plotting goes, this is book 7 in the series, and I have a feeling I may have missed book 6. There are definitely references to action that is unfamiliar to me. I was able to follow the book, nonetheless, but may have enjoyed it more if I'd planned my reading better. The series seems to have become more of a serial, and readers need to accept serials for what they are and plan their reading accordingly. I stumbled there.
Read 6 first!
Now I will go back to my own work in progress and its plotting that doesn't entirely satisfy me.