Organics will eventually create the Reapers, ergo the Reapers must prevent Organics from creating the Reapers. For their own sake, or some shit. By this logic, they should just TAKE OUT SYNTHETICS EVERY CYCLE instead of organics.
I think they cribbed heavily from the Spiral/Anti-Spiral arc of
Edit: I was just kind of semi-drunkenly making a joke about the whole "Take out synthetics every cycle" thing, but the more I think about it....the more I think this entirely invalidates the entire premise of the game. Instead of coming back and being all "We've deleted your AI's and VI's. No more of that shit or we'll have to destroy you, okay?" every fifty thousand years, they wipe out both synthetics and advanced organics? What? Why?