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.