Isnt that explained though? If what we saw wasnt an indoctrination and was a real explanation then it was that being of light (the little boy) that created the reapers. The reapers assimilate all the most advanced beings of the galaxy and in doing so only get stronger and smarter. They leave all the young races alone to grow but come to terminate them when they get too powerful. Thats why the cycle made sense but then it was broken through the efforts of Shepard. lol I almost wanted to let the reapers do whatever they wanted. Haha.
My one issue though is lol - who the hell are these beings of light and why arent THEY worth keeping under control.
Power On Self Test Yourself.