This is really what I was getting at regarding the ending. The ending suggests that it should have been a central theme throughout, but it wasn't. The places where it would've been possible to make it a central theme, it wasn't really even present. It simply shows up at the end and is supposed to be a big deal because projected hologram kid said so. "Synthetics will destroy all organics." Why? There is no reason. But they said it so it must be true. I am projecting my own desires for how I wanted the game to go onto that ending, I will admit. I love what that ending could have been.
So all in all, I believe this "synth vs organics" pretext at the end of the game was BS. The part of the game that revolves around it is way too small for it to justify the atrocities committed by the reapers. And it's not even the least bit explained.
The most emotional part of the synthesis ending is actually Joker and EDI, and has nothing to do with the Reapers or Earth or Shepard.