User blog comment:AdmiralPedro1stFleet/Goodbye Indoctrination and Hello Beings of Light/@comment-70.232.58.82-20120625212842

It is still messy plot-wise, but it basically works. It's not a question of it being good or bad; it's a question of it satisfying enough of the requirements of the narrative. It also sets up the conflict for future ME titles by positing an even greater enemy, which is also something Bioware needed.

Also worth noting is that the "Derelict Reaper" from ME2 from which you get the Reaper IFF was hinted at in exactly the same way, in an ME1 planet-scanning blurb. And look how important that became.

No doubt that the Beings of Light's solution is fundamentally flawed. They came up with the weird answer of reaping organics and  turning them into organic-machine hybrids  to "save" them from the fully machine race, the "machine devils"-- wherever they are. ("Machine Devils" are not Reapers.  The Beings of Light are the Reapers.  We have not met this fully machine enemy, the "Machine Devils"-- yet.)

At the end of ME3 the Catalyst acknowledges that he has "changed" and that Shepard and his effort has opened his eyes to a "new possible solution/s", which is an admission that maybe melting people into goo so that they could become hybrid beings to avoid the notice of a mysterious evil machine race wasn't the best idea.

It's not completely satisfying and far from perfect, but it works, basically. And that's good enough, since there is no lore-consistent anything that could possibly fill every last plot hole.

As for the Geth, who are fully machines, I guess one could argue that the Beings of Light/Reapers used a manipulable and not-so-advanced machine race as a tool to reach their larger goal of harvesting and hybridizing the organic races. Indeed, that's what Saren, who is obviously a hybrid creature under the control of the Beings of Light did. The Geth, just like Shepard initially, thought that the Reapers were completely machines. The heretic Geth worshiped Reapers, who aren't machines, but are hybrids of organics and machines; so it actually sort of makes sense that a Geth worshipping one would be heretical. Thus, the Geth were fooled by the Beings of Light/Reapers into believing they were just machines so that they could be used as footsoldiers in a larger Being of Light/Reaper plan to harvest organics.