The film itself is a well-told fantasy full of silliness and whimsy, but there's depth and meaning as well. It could be argued that this is a kids film about ethnic cleansing and genocide(!), but it's all handled in the best possible taste. Somehow they managed to pull this off without ever being too heavy or inappropriate. This isn't going to provoke nightmares or scar anyone for life, and is neither heavy-handed nor patronizing in getting its lesson across. An example of this would be the villain's henchmen, who spend much of the film in the mistaken belief that they're the good guys. It's not so much a film about good vs evil, as it is good vs foolishness.
It's also a world with a visible class system, where aloof aristocrats are so distracted with their ridiculous hobby that real world problems are neglected. There are interesting parallels to be drawn in this subtle bit of social commentary. From my perspective this was essentially apolitical, I don't expect any particular group to take offense at this. It shows the folly of aspiring to empty symbols of status.
There's more than enough going on in the film that you don't really have to think about any of this if you prefer to just sit back and be entertained. You could easily spend another viewing just taking in the beautifully detailed sets full of crooked buildings on cobble-stoned streets, and the immaculately tailored costumes, all of it so tactile and vivid in three dimensions you'll want to reach out. If you're the kind of person that would love to interact and play around with all these props and puppets, I recommend seeing it in 3d. It's like having them right there in front of you.
Aside from the window dressing, there's good characterisations all round. The Box Trolls themselves are particularly adorable, and endlessly amusing with their antics. Watching them bounce around and assemble themselves into various formations was a thrill. Expect some of the most inventive animation seen to date.
Stick around during the credit roll, there's a final post/mid credit scene that will make your jaw drop. The talent involved with the stop-motion animation makes this film a joy to behold.
Overall, I'd go so far as to say it's a future classic. It seems destined to be fondly remembered for years to come.