A question that bothered me every time I'm watching FMA\FMAB, it is clear that one body & soul had to be paid (plus arm), but why Al's and not Ed's? anytime I asked myself that I told myself that it happened to be that way, but it could be the opposite and Ed's body & soul to be taken and there's no special reason to that.
And that is my point, is there a reason or it really happens to be that way for no reason at all (except the author reasons of course ...).
What Truth takes is not arbitrary, but ironic; it takes something symbolic of what the alchemist who opened the gate desired. This is explained by Father in Chapter 102 of the manga (found in Volume 25), and is summarized by the FMA Wiki as:
Father discusses the irony behind the works of the 'Truth', who took Ed's way to 'stand by himself' and his 'only family', Al's body so he 'cannot feel the mother's warmth as he craved', Izumi's 'capacity to nurture the seed of life' and, now, with Mustang, coming full circle, 'depriving the man who had a grand vision to save his country of his eyesight, denying him to see what his beloved nation will become'.
As Brotherhood follows the manga, the reason stands there as well; in the 2003 anime, the reasoning may be similar, but likely exists simply because it was done in the manga, and the reasoning had not yet been revealed there.
Within your question, there is a false assumption, that "one body & soul" can be traded for another human life; human transmutation is not possible, and nothing was taken as any sort of equivalent exchange. Al's body was taken as the price of opening the gate, as was Ed's leg (his arm was not part of this exchange), Izumi's organs/reproductive system, and Mustang's eyes.
Furthermore, Al's soul was never part of the price. It was not taken by Truth; only his body was taken. It's shown within Brotherhood and the manga that Al's soul was what animated the failed human transmutation; it was the nearest thing close to a human (the chemical composition was correct) that shared a blood link to him. As the failed transmutation could not survive long term, Ed gave his arm not as part of the initial transmutation, but to force Al's soul onto the nearest human-shaped object and bind it before it was lost.
According to wikipedia
The only things Alchemists are forbidden from transmuting are humans and gold. There has never been a successful human transmutation; those who attempt it lose a part of their body and the result is a horrific inhuman mass. Attemptees are confronted by Truth (真理, Shinri), a pantheistic and semi-cerebral God-like being who tauntingly regulates all alchemy use and whose nigh-featureless appearance is relative to the person to whom Truth is conversing with; the series' antagonist, Father, and some other characters, claim and believe that Truth is a personal God who punishes the arrogant, a belief that Edward denies, citing a flaw in Father's interpretation of Truth's works.
so
After finishing their alchemy training under Izumi Curtis, the brothers attempt to bring their mother back with alchemy. But the transmutation backfires and in law with an equivalent exchange, Edward loses his left leg while Alphonse is dragged into the Gate of Truth. Edward sacrifices his right arm to retrieve Alphonse's soul, binding it to a suit of armor with a blood seal.
the better justification of equivalent trade is given on the blog dotandline.net
There is no equivalent exchange when it comes to love, life, or each other. In any kind of relationship, you can never truly pay anyone back. There is no convenient currency to barter with those who love us. Both Ed and Al give up everything for the other—and they wind up right where they started, though with a truer sense of what it means to be human, and to love. Each human being is just water, carbon, salt, iron, a handful of other ingredients, and everything we have ever felt. Every life we have ever changed. Every mistake we have ever made. Every person we can’t save. Every choice we can’t change. You can’t atone for what you’ve done. You won’t be rewarded for it, either, not in any sort of equivalent form. There is only the road ahead. The drive to keep learning, to do better, to bear the messiness it takes to keep on and gather the heartaches and small miracles you come across along the way. Sunsets, the wind on your skin, the harm you cause and good you’ll do, the risks you’ll take, everyone you’ve ever held or forsaken or made to feel alive—that, in itself, is a kind of magic.
