One theory is that of the "Happy Fault" (Felix Culpa). That is, sin, the fall etc were intended and in some sense "good", in that they allow for a process of repeated breaking and reconciling with the godhead, each time reconciling with greater and more sophisticated knowledge of the divine will.

Prayer and its effects act as a facilitator for this process, ie. God intends for the process of prayer to happen as it is a process of introspection and reconciliation, and as one reconcilies with the godhead, so does ones desires reconcile with the plan of god.