Turns out the Reapers are morons.
The Reason they're doing this whole cycle of extinctions thing is because they believe a technological singularity will inevitably cause AI's to be created, and that these AI's will see organics as too different to them to be related to, are thus a threat, and so will wipe out all organics on principal.
Apparently they think this way because they were built by an ancient race who suffered a Skynet like catastrophe.
These aliens were pricks.?
Rather than think they might have made a mistake when building this AI, handled their introductions badly, or just decided not to build anymore AI's, these ancient aliens decided synthetic life itself was at fault, because it couldn't possibly be anything else, and created The Reapers to kill all organic species before they got to a stage of technological advancement where they might start building AI's.
To sum up: they created machines that would wipe out all organic life in the galaxy, in order to prevent machines wiping out all organic life in the galaxy.
Now, this wasn't the original motivation for the Reapers. Originally, they were meant to be preventing dark energy coming in from outside the galaxy from prematurely causing all stars to die. That's why we had so many references to dark energy in ME2. The Reapers acted as giant energy sinks, which is why they sit outside the galaxy for 50,000 years, to act as a shirld. However, as time goes on the amount of Dark Energy increases, so they need to harvest more species to create more Reapers, hence the cycle. The reason they use intelligent species is to use the victims brain as a hive minded organic computer, in the holes of comming up with a more permanent solution eventually.
The end of the game would have given Shepard the choice of either blowing the Reapers apart and hoping everyone can come up with a new way to stop Dark Energy, or bargaining the Reapers down to just taking Humans for a new Reaper, and leaving everyone else alone.
Then ME1&2 Lead Writer Drew Karpyshyn left to work on SWTOR, and Mac Walter took over.
And apparently Mac is an appalling writer.
Not least of all for failing to remember that a significant portion of the last two games was spent teaching us that AI's are not inherently evil, and ME 3 proves the Reapers are wrong by having 2 AI's willing to live peacefully with organics, EDI and the Geth.
Hell, EDI even shags Joker. Which might kill him, but not intentionally.
So basically the Reapers entire motivation is flat out wrong, and means they're just irrational machines incapable of reasoning or thinking outside their programming, built by a bunch of insane, arrogant cowards.
Edited by Total Biscuit, 29 February 2012 - 10:52 AM.
No, I'm not 'that' TotalBiscuit.