The Boxtrolls is a very political movie. Of course, it isn't uncommon for a children's movie to be political - after all, a lot of kid's movies are based on fairy tales, and fairy tales regularly comment on class issues. (Sure, Cinderella wants to marry the prince because he's handsome and charming - but she also lives in a chimney while he lives in a castle.) What is rare, however, is that while most kids movies deal with political issues in a fairly straight forward manner The Boxtrolls approaches it's moral with a lot more subtlety.
There are three classes of people in the Boxtrolls' world: the aristocracy all wear white hats, the underclass wear red hats, and then there's a race of trolls that live underneath the city who wear nothing but boxes. Generally, people tolerate the trolls and their constant scavenging, but one day a small child disappears and the trolls are scapegoated for the kidnapping. A panic ensues, and a red hat named Snatcher sees his opportunity. He makes a deal with a white hat named Lord Portley-Rind that if he can round up all the trolls and neutralize them he will earn a white hat for himself, which will mean he'll finally earn access to all the fancy cheese eating parties that are exclusively for the aristocracy.
Now, I'm not claiming that the entire movie is subtle. The movie's plot unfolds in a fairly predictable manner - Snatcher's secret motive is revealed at the exact time you might expect it to be revealed, and of course he gets his just desserts like villains always do in kid's movies. But the political implications of this story are, in fact, very subtle. Most kids movies operate on a simple good and evil binary, which is fine, because that means that kids can immediately grasp what the story is trying to do. However, the Boxtrolls is actually based on a shades-of-grey three tiered system because it makes a distinction between the apathetic class of aristocrats and the actively malevolent villain. That's important, because that allows the film's political metaphors to come much closer to describing how politics actually works.
The best way to explain explain why I think our political system is actually three tiered is probably to use an example I learned from Nixonland, a book that focuses on American politics from 1965-1972. That was a time period where there was a lot of racial unrest, and before I read that book I knew about people like George Wallace who were willing to stand in front of a news camera and talk about how much they loved segregation, and I knew about any number of blatant examples of cruelty, like the police attacks on the Selma marchers in 1965. But I didn't have much of a sense of the complete picture, because the people who were up front about their biases provided a lot of cover for people who had the same agenda but who understood the value of doing their work in the shadows.
For example, I doubt many people that aren't from Chicago would still recognize Mayor Daley's name, but he was just as staunch a segregationist as his southern compatriots - he just didn't announce it on the nightly news. By slowly manipulating the city's zoning laws, strategically placing freeway on-ramps and off-ramps, and monkeying with the city's bus routes Daley managed to isolate certain neighborhoods and open up others, leading to de facto segregation. Daley managed to completely isolate Chicago's black communities all while still earning the vast majority of their vote because most people didn't understand what he was doing; the only way to see the cumulative effect of all of his policies was to pay attention to the little nuts and bolts of boring issues like zoning laws, which most people aren't going to do. Nixonland makes it clear that George Wallace's crime wasn't being hateful, it was being hasty. If Wallace had acted slowly and been more savvy about protecting his public persona he might have gotten away with his agenda just like Daley did. But no; he had to trumpet his agenda to the nation like an idiot, and as such, he's still a national punching bag, while Daley's descendants remained powerhouses in Illinois long after he died.
The reason why I think that the Boxtrolls' three layered structure is a lot more accurate depiction of our politics is because it makes room for both Wallaces and Daleys. Snatcher is the obvious villain of the movie because he's the guy who roams around the city harassing the poor trolls, but he's ultimately doing it on behalf of Lord Portley-Rind. When you compare the two characters subtle moral differences come to the fore that actually turn Portley-Rind into the real villain. After all, Snatcher has something to gain by persecuting the trolls because that's the only way he can get into the upper class while Portley-Rind allows the trolls to be destroyed out of casual disinterest, which is much worse. Snatcher's spite might be misguided, but you could see how his enthusiasm could have lead to something good if it had been directed at a more positive goal, but it's pretty hard to justify Portley-Rind's obsession with fancy parties and total apathy towards the suffering of other people.
I doubt kids will understand the true villain of this movie when they watch it; Snatcher is such a classic villain enacting such a classically villainous plan that he's the obvious target for scorn. But if those kids take a second look at this film once they've grown up, they might see a completely different picture - one where the true scoundrel is not the man in the middle who is trying to keep the people at the bottom down, but rather the man at the top who is using the man in the middle to keep the people at the bottom down so he can continue a life of luxury completely unfettered by unwelcome distractions. In other words, they will see a movie that has a lot more to say about the world they actually live in than a movie that pretends that our moral choices are between "evil witches" and "handsome princes."