I think they pretty much stopped caring about having the story making sense after they finished ME2. There are a ton of huge plot holes long before the ending stretching back to "The Arrival."
The main plot hook of "The Arrival" is a plot hole. The Reapers have always tried to hide their existence. They make sure that no one can learn of their existence so no one can prepare for their invasion. If it wasn't for the Prothean Beacon, no one would know about the Reapers. In fact, much of the first game was about Saren/Sovereign trying to stop Shepard from learning about the Reapers. So why would the Reapers leave behind an artifact that not only revealed their existence but also gave information on their secret back up plan to invade the galaxy?
Not to mention how the Reaper invasion of earth is a plot hole. It's revealed in ME1 that the Reapers can shut down the Mass Relay network with the Citadel. In fact, in the final ME1 mission, Saren had shut down the Relays and Shepard had to turn the Relays back on to let the Alliance reinforcements through. So why didn't the Reapers just shut down the Relays to prevent the Victory fleet from attacking?
As for the whole organics vs. synthetics thing, I have to say that it's likely that the Star Child has a lot more experience. After all, just because the Quarians and Geth made peace doesn't mean the peace will last forever. It's entirely possible that the creator of the Reapers have seen such alliances break down in the past.
The main plot hook of "The Arrival" is a plot hole. The Reapers have always tried to hide their existence. They make sure that no one can learn of their existence so no one can prepare for their invasion. If it wasn't for the Prothean Beacon, no one would know about the Reapers. In fact, much of the first game was about Saren/Sovereign trying to stop Shepard from learning about the Reapers. So why would the Reapers leave behind an artifact that not only revealed their existence but also gave information on their secret back up plan to invade the galaxy?
Not to mention how the Reaper invasion of earth is a plot hole. It's revealed in ME1 that the Reapers can shut down the Mass Relay network with the Citadel. In fact, in the final ME1 mission, Saren had shut down the Relays and Shepard had to turn the Relays back on to let the Alliance reinforcements through. So why didn't the Reapers just shut down the Relays to prevent the Victory fleet from attacking?
As for the whole organics vs. synthetics thing, I have to say that it's likely that the Star Child has a lot more experience. After all, just because the Quarians and Geth made peace doesn't mean the peace will last forever. It's entirely possible that the creator of the Reapers have seen such alliances break down in the past.