It means that literally THE ENTIRE SERIES is based off bullcrap. This entire series has been Shepard vs the Reapers, and the Reapers have NO REAL LOGICAL reason to exist or attack. I'm sure that if I sat down with ANYONE in this thread for 8 hours, we could brainstorm and come up with a better reason than this for the Reapers existing, and doing this cycle of extermination.
I think the reaper's motivations for the cycle can be salvaged if we dump absolutely everything about synthetics from the ending. The whole "Galactic history is a cycle, reapers use harvest to prevent the end result of that cycle" thing basically works, it's just that the end result their trying to prevent (evil synthetics) is absurd.
A few alternative motivations for the reapers:
1. Dark Energy, wooooo! The Reapers have determined that the Universe is in store for the big rip, that is, the sundering of all matter by universal expansion. The Reapers believe that the manipulation of Dark Energy is vital to controlling and eventually preventing the effects of the Big Rip and Universal expansion. They use the galaxy as a giant lab, encouraging the test subjects to develop Mass effect technology and other means of manipulating Dark matter in the hopes of gathering up innovations that the Reapers themselves have been unable to devise. The Reapers use the biomass of the various species in each cycle for reproduction in order to ensure the continuity of their project. The reapers do not simply inform intelligent life of what their doing because they believe that the galaxy's inhabitants are too short-sighted to actually work towards a solution for a problem they won't be dealing with for billions of years.
2. arrogance: The Reapers believe themselves the pinnacle of everything, the ultimate anything that anything could be. You should be honored to be harvested and turned into a reaper. Their doing life a favor by bringing it up to the glorious pedestal of reaperdom. It's just so much
better than being a squishy humanoid. You just can't understand how wonderous it is.
3. The Ultimate predictive model for life: The Reapers seek to create an all encompassing scientific model of life itself. The galaxy is their laboratory, and in each cycle the reapers change one or two variables, while keeping things like Mass Relays as constants. The reaper harvest is the ending of the experiment, where the reapers wipe the board for the next set of test subjects, and reproduce. No one told them they can simply work backwards from 42.