Fullmetal Alchemist: Brotherhood centers around the alchemist's struggle to obtain the ultimate knowledge that lies behind the Truth (with a capital T). Those who are successful in their search are those who demonstrate an understanding and compassion for their fellow human beings.
The Truth first appears as a mysterious white sprite enveloped in black, and is someone who seems to have all the answers whever Edward or Alphonse find themselves inside the portal of truth. When Father (also known as the Dwarf in the Flask), Fullmetal Alchemist: Brotherhood's main antagonist, ultimately fails in his goal to become God, he asks the Truth, "Who the hell do you think you are?" to which the Truth responds, "I'm the existence which you all refer to as 'the world'"
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How Characters View Others
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Father goes about his goal of becoming God by purging himself of the sins of man (Lust, Gluttony, Envy, Greed, Sloth, Wrath, and Pride), and he treats other human beings as objects to be observed rather than creatures with their own unique sets of beliefs and experiences. In contrast, Edward and Alphonse Elric realize with the help of their teacher that "One is All and All is One" early in their alchemy training. A realization that enables them to see even the smallest ant as a part of the larger world. These two different approaches to unlocking the Truth are also present in each alchemist's approach to the philosopher's stone.
Father, Kimblee, and pretty much every other villain from Fullmetal Alchemist: Brotherhood view the philosopher's stone as a weapon or tool that can be used to enforce the user's will. None of the show's antagonists care at all about the human sacrifice that's necessary to fuel their war machine. On the other hand, Edward and Alphonse never take human lives for granted. Hoenhiem (Ed and Al's father) spends years learning the names and details of the thousands of human beings inside of him, the humans that fuel the philosopher's stone that is his body. Heinkel and Dr. Marcoh tell Al that it is okay for him to use the philosophers stone in his fight with Kimblee and Pride because he recognizes that there are people inside the philosopher's stone and that those people would want to protect what's closest to them. Edward refuses to use the philosopher's stone in order to return his original bodies back because he sees that as making others pay for his mistakes.
Who Owns the Truth
The reason why the heroes' and the villains' approach to gaining unlocking the Truth comes down to their motivations for doing so. Father and the homonculi view obtaining the Truth as instrumental in their desire for power and dominance over others. State Alchemists, the branch of the military devoted to 'research', is really just a place to harvest sacrifices or weapons. Father wants to become God so that he can be perfect. Edward and Alphonse view understanding the Truth as intrinsically valuable, or something that will enrich all of humanity. But what is it that makes the heroes value knowledge not as a weapon, and why are the villains only interested in knowledge as a way to assert their own superiority? What is it that Father lacks which Hoenhiem possesses? Empathy. The answer is empathy.
The humans fighting against Father all care about each other, and they care about the citizens of Amestris. They care about the people trapped in philosopher's stones, and they even care about the show's villains. All of this to say that people like Edward and Alphonse care deeply about the world, and Father wants to destroy and remake the world in his own image. Which brings back the moment when The Truth states that he is the world, and every living creature, and Edward Elric, and Father are all a part of the world. What makes someone intelligent in Fullmetal Alchemist: Brotherhood is their ability to empathize and understand others. Each person has their own unique experience and perspective on the Truth, and intelligence lies in being able to see the Truth through the eyes of as many people as one can.
Fullmetal Alchemist: Brotherhood teaches a valuable lesson on what true intelligence is. Like Father, there are plenty of people in the world who use their knowledge as a weapon to assert their own intellectual dominance over others, but those people are not intelligent. A truly intelligent person will use their knowledge to find commonalities with those around them, and be able to understand perspectives that are different from their own. Empathy is what makes Hoenhiem, Edward, and Alphonse the most intelligent characters in Fullmetal Alchemist: Brotherhood.
What is Intelligence?
There are some who would argue that Father was in fact more intelligent than Hoenhiem or the others. That his morals and ethics have no bearing on his intellect. Father does demonstrate many feats of raw destruction and everlasting life might be enough to justify his arrogant attitude. Could Father have succeeded in his plan to acquire the Truth even though he lacked a shred of empathy? Probably not with intelligence.