The Boy and the Heron

 Like a lot of Japanese films by Miyazaki, to understand the Boy and the Heron requires cultural background so will need several watchings, 

but visually it is beautiful.

and many of the themes are universal: not fitting in your world, questing through danger, and seeking your lost mother, and of course the way greed and power over nature results in distorting the good people into monsters: 

the uncle used the magic stone from outer space in order to make realities: but what he actually has done is to make realities full of horrors, 

an example of how the uncle's manipulation has resulted in horror is shown in the sequence of the pelicans who kill the innocent warawara because they have no other way to survive. (the Warawara  are "unborn human souls who reside in the Sea World. Once they mature, they fly up into the sky to be born as humans.") 

Behind all this symbolism is the story is about a middle school boy who leaves Tokyo after his mother dies in a bombing, and who is having trouble adjusting. 

But when his stepmother goes missing, he goes to rescue her, and enters a strange magical tower meeting all sorts of weird animals and helpful people, including the fire girl Lady Himi, who turns out to be his mother, who entered the tower from a different time line and must return to that timeline before the tower crumbles.

according to this discussion on the CBC, Miazaki made the film as a way to teach his grandson. And ironically it is inspired by a book about a boy seeking truth, but unlike Miyazaki it was written before WWII...

The story of The Boy and the Heron is inspired by the Japanese classic novel How Do You Live?, but they don't tell the same story; the book follows 15-year-old "Copper" (nicknamed after Copernicus) in the wake of his father's death. In a series of vignettes, he questions whether a classmate is a lesser person because he lives in poverty, experiences how to be a good friend in difficult situations and wonders what makes a person great. ,,,

the details are different but the theme is the same: Young people seeking the meaning in life and what is meaningful in living. 

Another theme is mourning death of a loved one:  the voice he follows turns out to be his mother, the fire lady.

and that is what I take from the film: That we confront life but it is through our relationships that we find redemption.

The Shinto love of nature is not as strong in this film as in previous ones by Miyazaki, but it is there:

Earthday website explains this aspect of the film: 

 Everything in this place, we learn — from the land to the sea, including the Grey Heron himself, after whom the film is named — is managed by Mahito’s Granduncle, a Wizard-of-Oz-like sorcerer who receives his power from a magical stone, which fell from the sky decades ago and possesses awesome properties. In a way, one could say that, through the stone, Granduncle serves as the steward of nature’s power. Without the stone, a (super)natural object, Granduncle is no more than a man; with it, he becomes a godlike figure, able to shape the world in whatever image he chooses.

There are a lot of explanations on Youtube, but most of them seem to be from a western point of view, whereas Miyazaki infuses his worlds with Shinto symbolism and Japanese way of thinking