The way I remember it - the universe was dying of entropy. The Reapers were created to solve the problem of entropy, but could not do so by the time of the events of Mass Effect. The purpose of the Reapers was to combine the intelligence of each species in order to attempt to solve the problem. Each cycle, species would be harvested to add to the computing power of the Reaper fleet.
The final choice of the series was to be: 1. Acquiesce to the demands of the Reapers, and join them in their quest to save the universe; or 2. Do not acquiesce, end the cycle of destruction, and trust that the races of the galaxy will be able to solve the problem.
This is an infinitely better ending than what we got. Although...the indoctrination theory would have been breathtaking as well. Too bad BioWare wasn't that clever.