Chief among its faults was a odd sort pacing that made the story feel both sluggish and contrived. Second was that it attempted to focus on too many characters. That can be done and it can be done well, but in a horror-fantasy-superhero action flick, where each of those genres are already demanding a fair chunk of your screen time, it's a no win situation. There was good drama to be had in the story, but with the limited amount of time to play it out on screen, it was like watching it through binoculars. Lastly, and this is much more of a personal bias, I find that the more elements of fantasy you put in a story, the less special they become, and each of those fantasy elements palpably drain away the tension you're working to create, because the audience know that any bad magic that happens will be easily undone by some other magic sooner or later. And, of course, there were a handful or irritating plot holes and poorly thought through devices, but nothing I found too ruining.
That said, the movie looks gorgeous. The special effects and art design were fantastic. An extended cgi puppetry scene was pure delight. And Guillermo Del Toro (fresh off his amazing Pan's Labyrinth) can do something rarely seen: make an action sequence that is poignant and affecting. There's really so much to commend in this movie, so much that makes it worth seeing, which makes it all the sadder that the final product is so damn inert.