Fullmetal Alchemist: Brotherhood is routinely classified as one of the best anime ever made, and for good reason. Not only is it an exciting, action-packed shonen series with fabulous character development, it also has some seriously deep symbolism that adds an extra layer of intrigue.
Some symbolism seems obvious; most viewers understand the Homunculi are named after the Seven Cardinal Sins. However, it's easier to miss the way all Homunculi (aside from Gluttony) punish people who commit the sin they represent but are ultimately wiped out by the same sin.
Other bits of symbolism are more subtle, like the connection between Truth, the Gate, and a religious philosophical movement called theosophy.
Hoenheim is the human manifestation of a Philosopher's Stone, but he may also symbolize Jesus Christ. This isn't uncommon in literature and other media - Christ symbolism appears in everything from Dostoevsky's The Idiot to DC Comics' Superman.
In Hoenheim's case, the symbolism appears when he needs to cross a flooded passageway to reach Father's transmutation circle. Rather than draining the passage, he opts to use alchemy to walk across the water, an obvious allusion to Christ.
In addition to Hoenheim's Christlike persona, FMA references another key figure from Christian mythology: Lucifer. Initially, Lucifer was an angel and revered for his wisdom, but he was kicked out of Heaven after God decided he was too ambitious and proud. Rather than accepting his banishment and retreating into the shadows, Lucifer proceeded to tempt humans with forbidden knowledge, and eventually went on to rule over Hell, where he is known as Satan.
How does this relate to FMA? The Gate of Truth created Father (the show's ultimate antagonist), but the villain ends up existing in the mortal realm. He's lauded for his knowledge of alchemy and he tries to share his expertise with mankind, but in doing so, he strives to become greater than the Truth, or God.
Are our souls inhabiting a body, or is that body our humanity? According to FMA, and to philosopher René Descartes, the former is true. The mind and the body are distinct entities, and the destruction of the body does not mean the mind is also gone.
While most people accept that Ed is still Ed after losing an arm and a leg, things get more complicated with Alphonse, who loses his entire body, including his brain.
In FMA, many people don't see Al as human because he doesn't eat, cry, or perform other physical functions that one might expect from a human being. He has to constantly affirm his own humanity, which clearly exists in the form of opinions, emotions, and memories.
Theosophy is a school of thought that merges teachings from various religions and philosophies with the intention of arriving at truths about the meaning of life, the nature of God, and other big questions. Two concepts from theosophy make themselves known in FMA: the Monad and the Akashic Record.
The Monad is actually a combination of two theosophical principals: Atman and Buddhi, which roughly mean spirit and spiritual awareness, respectively. Basically, the Atman is an image of God, while the Buddhi is an interpretation of that image. They combine to create an all-knowing being called One, which closely resembles the Truth in FMA.
When Ed forcibly is pulled into the Gate of Truth, a film strip containing all the world's knowledge ends up in his head. Though this is painful, he recognizes it as the ultimate truth. This is analogous to the Akashic Records, which are a recording of everything that has ever happened and every bit of knowledge that exists in the world.