I've always thought of the Reapers as a personification of the natural cycles of birth and death that plague all civilizations. Some upstart always comes along and surpasses and/or destroys every Great Civilization. In this light, perhaps we can view Technology (i.e. the Reapers, but also the Geth etc.) as the upstart competition. (Interesting that we create our own competition, but that's another topic.)
Not surprisingly, when Shepard confronts this unstoppable cosmic force, he is utterly powerless to challenge it. He must simply accept its terms. I think Bioware wrote this into ME3; the tone throughout the story is bleak and contains strong elements of resignation and fatalism. Some forces are greater than even Commander Shepard. Our hero learns this lesson and is terrifically humbled.
At the end, the choices all civilizations must face are presented to Shepard. A) We can destroy the competition/upstart. I'm thinking here of genocide, Rome salting the earth of Carthage.

We can assimilate the competition. This, I think, is closer to how most historical cycles proceed. Rome sucked up everything Greece had to offer, which was a lot; likewise the American-European dynamic. C) We can enslave the competition, turn them into puppet states. Lots of examples in history for this. Colonialism is the most recent incarnation of this trend. None of these options is really Paragon. They all contain a degree of Renegade. Sounds like history. For me, Synthesis-assimilation is the most morally acceptable ending.