User blog comment:The Milkman/Reaper Logic/@comment-4950455-20120423230902

''Another point: What exactly are the Reapers accomplishing? They're Synthetics who aim to kill all intelligent Organics. What is the difference between them and the Reapers? By creating the Reapers, all God Kid accomplishes is the death of Organics by different Synthetics. Good job.''

This is the one point I think does have an answer - it's made pretty clear that the Reapers/Catalyst feel that by melting down organics to make new Reapers, they're preserving them in some fashion. "Normal" hostile synthetics, on the other hand, would be assumed to simply wipe them out altogether. There do seem to be some hints in the lore that part of the consciousness of the people used to make a Reaper lingers inside it.

Not that this makes the other points less valid. Heck, I'm pretty sure Javik even says/implies that his cycle's geth-equivalents were, while hostile on their own, made more of a threat by the Reapers. Beefing up the other side is sure a great way to preserve organic life, isn't it?