So I finally finished the trilogy a few days ago. I initially fukked up with the Suicide Mission and got half the crew killed, so I cheated and looked up how to keep everyone alive. Zaeed was the only member that wasn't loyal and didn't realize that it would get him killed in ME3
I picked the destroy ending, but can definitely see why a lot of people were pissed about the ending as the info dump at the ending with the little dude had no final boss essentially.
I guess my main question is how did Shep and the crew manage to not end up being indoctrinated at any point with how much contact they came in with reaper tech? The game was rather inconsistent and not entirely clear in how the concept worked as I left Rana alive in ME1 on Virmire for her to only end up killing people years later in ME3.