Nah I think grey_wind is right on the money.
In making a coherent story, IF it were a good idea to say that synthetics and organics always had to war, there need to be A LOT more groundwork for that. One way certainly is to make sure the quarians and the geth cannot achieve peace. That is actually the best way, as far as I'm concerned. And for some reason, beyond comprehension, if someone wanted to leave that in there and yet prove that synthetics and organics would eventually come to war...which it seems the writers wanted, then they didn't do enough to explain why the peace didn't matter.
Sorry a suddenly appearing Glowjob's word for it isn't enough. Unless Shepard became super stupid. I mean, I already have a hard time with Shepard not saying something intelligent as a retort to Glowjob. But it sure is a lot easier to believe Glowjob if what he says isn't immediately refuted by events that occur right inside the same video game.
You lay the groundwork for these things to make your ending clear, and your speculations coherent, as opposed to looking like you blew it (which, sorry, ME3 did).