Mass effect 3 ending spoilers here.
So the kid in the ending states that the whole Reapers thing is to cull Organic life to save the Galaxy from Synthetics taking over. But until that point there's no indication that Synethics actually do this except for the Reapers (Ironic) that I'm aware of. I didn't play ME 1 or 2 however. The Geth were proven to be peaceful and acted defensively when you go through the Quarian Homeworld part, unless it was a fabrication.
So…what evidence exists of Synthetics actually being bad, or is this (another) plot hole?
Best Answer
The way the child phrases things, it's not an issue of "who?", but an issue of "we can't take that chance".
Back before the Reapers, presumably, some civilization built a synthetic civilization, and it went rogue. The response to this was to prevent any civilization from ever advancing far enough to build a synthetic civilization again.
The Reaper Child isn't looking at any one thing in particular and saying, "That's bad, we should kill it", but rather, "Everything has the potential to do bad things, so we should preemptively kill it".
The problem in many minds, is that evidence in the Mass Effect series points to the opposite - the fact that the Quarian / Geth resolution can even exist seems to fly right above the head of our spectral reaper-child. Not to mention the literal anthropomorphization of EDI, and her interactions with Shepard and joker. The only evidence the player has had up until this point of a synthetic enemy threat, is the Reapers themselves.
The only evidence that the Catalyst's final solution is necessary... was engendered by the Catalyst itself.
Or, in Xzibit's words...