I really disliked some of the ghostwriting (some of it I loved), the helmacrons, and the incredibly abrupt introduction of The One on the last book. Oh, and the lack of editing (KASUs anyone) bugged me, though I understand that particularly with later books, the production schedule was so fast that they just didn't have time.
I LOVED the character development and character-driven aspects, I loved the mechanics of the morphing and, well, all of the technology -- I loved the dream sequences, hell, I even usually love the filler (Cassie's Australian Adventure, anyone? I actually enjoyed the hell out of that book.) Oh, and I LOVE the Chronicles books, all of them. And the time travel. And the animal psyches. And MOST THINGS.