So I'm hearing news from the SomethingAwful forums that the journalist who is playing the advance copy of ME3 is letting loose some gossip heard at Bioware: that the reason for the Reapers' cycle was something that was dramatically changed after Drew Karpyshyn was transferred to the Star Wars team.
The original motivation for the Reapers was as follows.
"The Reapers' goal was to find a way to stop the spread of Dark Energy which would eventually consume everything. That's why there was so much foreshadowing about Dark Energy in ME2.
The Reapers as a whole were 'nations' of people who had fused together in the most horrific way possible to help find a way to stop the spread of the Dark Energy. The real reason for the Human Reaper was supposed to be the Reapers saving throw because they had run out of time. Humanity in Mass Effect is supposedly unique because of it's genetic diversity and represented the universe's best chance at stopping Dark Energy's spread.
The original final choice was going to be "Kill the Reapers and put your faith in the races of the galaxy in finding another way to stop the spread with what little time is left" or "Sacrifice humanity, allowing them to be horrifically processed in hopes that the end result will justify the means."
(The SomethingAwful guy then goes on to say that all the foreshadowing about dark energy in ME2 (including Haestrom) is never brought up again in ME3.)
The Reapers new motivation is as follows.
(Most of this paraphrased from what a guy on BSN said)
The Reapers new goal is that they are working to prevent a technological singularity. The quick definition of a "technological singularity" is basically a point when the machines of a civilization become more advanced than their creators and they are able to outdo their creators in pretty much every way imaginable.
The game attempts to justify the Singularity Motivation because all it takes is ONE incident with A.I. to bring about an apocalyptic war that would destroy all organics. Project Overlord was a very, very clear example of this: Cerberus nearly destroyed the entire galaxy. Organics lucked out big time that the Geth were so understanding and that A.I. like EDI are tame (and even then, EDI did something in the past before ME2 that may make you view her in a very different light: Mass Effect 3 reveals this).
The Reapers aren't hypocrites (in concept) in the Singularity Motivation because they don't perceive themselves as machines wiping out organics. They see themselves as immortal vessels that preserve a civilization forever that just happens to be synthetic. They see themselves as the saviors of organics for letting them grow and prosper and then harvesting them before they evolve to the point of singularity. "Imposing order on the chaos of organic evolution" as Sovereign said.
People say over and over that the Mass Effect trilogy was planned out in meticulous detail when it launched. While they may still be following the outline they had at one point, it is clear that the change up of the writing team during Mass Effect 2 left the story flailing in the wind significantly.
At this point, there are only 2 writers from Mass Effect 1 still with the series: Mac Walters and Patrick Weekes. Please look at what happened to all the writers from the ME series:
ME1
Drew Karpyshyn (lead writer) - went to Bioware Austin sometime during ME2's development; he quit Bioware on Feb. 15, 2012, and left the video game industry
Chris L'Etoile - quit Bioware in 2008 to go to ZeniMax Online (the parent company of Bethesda)
Luke Kristjanson - moved to Dragon Age team
Patrick Weekes - still writes for Mass Effect games
Mac Walters - still writes for Mass Effect series, currently lead writer as of ME2
ME2 (In addition to those listed above, ME2 has these writers on the credits):
Malcolm Azania - left Bioware for Maxis
Chris Hepler- Unknown
Brian Kindregan - left Bioware for Blizzard
Jay Turner - Unknown
Therefore of all the original ME1 writers, only 2 remain (Patrick Weekes and Mac Walters). And Patrick Weekes didn't even do much for ME1.
In any case, what we can say for certain is that Bioware did not have such a significant change in the story planned out from day one.
http://www.ign.com/boards/threads/somethingawful-the-plot-of-me3-changed-dramatically-big-big-spoilers.250066288/