nice answers to what the so6p found his motives. it's fun to think about imo. if i may add my take and see what you guys think.
anyway, pein is somewhat central to my idea. remember, there are two labels that are sometimes seen as one and the same yet contextually have proven to carry distinctions of difference. i am talking about "the child of prophecy" and "the reincarnation of the so6p". first, let me put those labels under abstraction to illustrate a point. so6p = question, child of prophecy = answer. now, the reincarnation of so6p was indeed pein, not only because madara's eyes allowed nagato to enjoy so6p bursts of power and method used by so6p as well as them being obviously the same type of eyes so6p possessed (rinnegan) but because pein as "question" is identical to so6p as "question". i believe so6p, after the ordeal of the jyubi and spreading ninjutsu, was searching for a solution to solve crisis in humanity. since he gave humanity a gift more or less constituting weapons, he had hoped humans would understand each other by experiencing the same pains. so6p was not, however, hopeless nor evil, at least in depictions so far offered so his solution was more deterrent in nature, a reminder what out of control power can bring upon humanity. he had gotten as far as what was his possible limit but created the stage for humanity to ask itself the types of questions jiraya, nagato, and yohiko suffered in search of answer. i hold to this idea because akatsuki, both of the organizations intentions, one overt and the other secret, are the two ways the so6p would have weighed during the imparting of ninjutsu; 1) monopolizing power to be a deterrent against further war and 2) to inflict pain as the medium of human empathy. the reason there needs to be a reincarnation of so6p in the first place is to ensure the "question" is posed properly to the child of prophecy so that he may form the "answer". this is exactly what took place and was realized when naruto met nagato's challenge and satisfied the dilemma dogging humanity since so6p himself first faced it.
naruto is, of course, the child of prophecy not only because the manga outright said so but because he fits the question's puzzle perfectly.
furthermore, this frees naruto from any expectations we might have regarding naruto inheriting any of the so6p powers. by not being the reincarnation of so6p he will, by virtue of being a product of his era, develop powers necessarily different from so6p and fitting for application against the "old problems". a new power is likely required to complete and conclude what began with so6p and redefine humanity for its place and role within the next era. don't hold your breath for the child of prophecy to simply mimic so6p to resolve so6p legacy, it wouldn't work.
i am not forgetting that any of this is subject to ruin but with so little to go by regarding so6p life and his generation's struggles.. pein was an obvious symbol of so6p that his questions would completely justify the so6p's mark left upon the world and bestowing ninjutsu, tailed beasts, and deposits of power within many bloodlines. otherwise, most motives anyone attributes to so6p would be weak and in demand of scrutiny.
p.s. and the first introduction to kyubi, it was said it appeared in times of humanity's ugliness but later seemed untrue due to technical evidence by which it appeared and some others. it actually is still truth, though, as the jyubi would be the hubris born prospect of doom. humanity likely was on the verge of absolute corruption so the shinobi world was created so that a new understanding of power would emerge and help keep humanity on a path where hope still treads.