It's unfortunate, there was originally a whole "dark energy" storyline that was supposed to provide an actual justification for the reapers and become the main story after they were gone. If I remember right, the gist was that the mass relay-based tech that keeps being re-developed in every cycle effects space-time in a way that would threaten life across the universe if it was used at too big of a scale, so the reapers regularly purge advanced civilizations to keep it from getting developed too much, to preserve life in the rest of the universe. But we would only find this out after stopping the reapers, so then the story becomes finding a way to stop it from happening without having to resort to cyclical genocide. They started hinting at it in ME2 so they could do the big plot twist in ME3, but then there was a change in the writing staff after 2 came out, and between that and 3 being rushed so much, it was never picked back up. Except for the sort of half-assed reworking of it for the plot of Andromeda lol