The Reapers are meant to represent the fear of the unknown (notice the name "Reaper" it means more than simply someone reaping things in, it is representing death and all of death's unknowns). The Mass Effect series is based around defeating a smaller insurgent. The insurgency is controlled by the reapers. The narrative arc is designed to show that you're only fighting a battle, not the war. And the mystery of the reapers is what makes them, to me, interesting.