Throughout Fullmetal Alchemist, the message has been sent that you cannot create something from nothing. This concept, equivalent trade, is what Edward knows and accepts to be the truth of the world. Alchemy is a science in which you change one thing into something else, but you cannot make something of lesser value into something of greater value... not in the technical sense, anyway.
As the story progresses, I began to realize more and more how the classic argument of "Nature vs. God" springs up, and how the use of this argument in the case of Ed is very ironic. Ed treats alchemy as his religion.. it is his belief and his way of life. He is determined that with the proper sacrifice he can get exactly what he wants in return as long as it has the same worth.
The moment his mother became a homonculus, the truth of his beliefs in alchemy became a jumbled mess of "what if everything I ever learned was a lie?". We can logically assume that once his mother died, her soul left her body and that there is no possible way to restore it. That is something that science is incapable of. To say that humans have souls is in itself assuming that a God exists and is proof that no matter what you sacrifice, you cannot create or transmute a human soul using alchemy because only God can do that. (You could try and say that maybe a soul is something scientific, but that would probably just be "conciousness". The meaning of soul is erased when you make it into something scientific.) While this should seem "obvious" after Ed and Al's big accident, Ed continued to believe that alchemy would get him back something that is worth exactly what he lost. At the same time, he had accepted that you cannot create life using alchemy; you can only alter it, and usually only for the worst. He also accepted that he had "sinned". In a Godless world, is there such thing as sin?
I think that this whole time, Ed's hope of restoring Al to his body has been out of desperation and denial. He has entirely blocked the possibility of failure out of his mind. He is using his own blind faith in alchemy and hope to motivate him in his search to restore his brother. If it weren't for the fact that Ed managed to bind Al's soul to an object, I'd say there's absolutely no possible way Al will be restored. I believe this series emphasizes that our soul is what makes us human, and that no science will ever change that. Ed knows this, and it tears him up inside because it contradicts the main laws of alchemy and science in general, but alchemy is in a way "all he knows" so he feels that much of his life until now has been lived a lie. I think it is the acceptance of his sin and the love for his brother that will ultimately save him from destruction.
When I reflect upon it, I feel that Ed should have realized a lot earlier that saving Al's life via binding his soul into armor in the beginning was not so much an equivalent trade. Ed sacrificed an arm and a leg but is that the actual worth of a human soul? I doubt it. I think maybe there was some divine intervention back there, somehow, because you cannot put any scientific worth on a human soul. Maybe a body, but not a soul. Even if the trade was Ed's mother's dead body plus his arm and leg I doubt you could say that was worth the saving of one soul. You could also assume that maybe he gave his mother's empty shell and in return was able to give Al's soul a shell of it's own to reside in, but while Al's body was pulled beyond the gates, his mother's body remained where it was, a hulking mass of fried something-or-other. It's very hard to make out exactly what Ed sacrificed aside from two of his limbs to save his brother, but we KNOW that a soul is worth more than that.. or less, depending on how you see it. A soul is priceless but at the same time it has no scientific worth because it does not exist in Science. Therefore is it really possible to bind a soul with alchemy? It almost suggests that Ed binding Al's soul did not in fact involve alchemy at all.
As far as I can contemplate, to combine the soul with science seems contradictory... downright impossible even. Whatever it is that is able to transport a soul in this series, I don't think it's alchemy, but something else unspoken. The same something that voids the law of equivalent trade.
In conclusion, my brain hurts.