I know all that. I'm saying that they can be fully Indoctrinated, and the Reaper capable of exerting more control, but it applies only subtle control to allow the subject more utility. You're saying that the Reapers were not capable of fully controlling Saren or TIM. Ultimately, it makes little difference. As for the brain, only the synthetic parts would be immune. We don't know what a synthesized brain is like or how it functions so we don't know what affect Indoctrination would have on it. Not all parts of the brain are equally important or do the same things.
I notice you ignored the Citadel Relay function, the most important thing. Which is funny since you accuse me of looking for things to argue. More projection. More importantly it shows even more that you don't have an answer. Anyway, the control of the arms was critical enough in the first game. Sovereign needed them open to get in but he or Saren immediately closed them again to protect Sovereign.
They can not control strong willed people fully. Think of what you will of both TIM and Saren they were both strong willed individuals. This was also shown with Liara's mother. They were able to temporarily break the indoctrination hold on on them to kill themselves rather then let themselves continue to be used as puppets. And in both TIM and Saren's case this is after they were "upgraded" with Reaper tech in their bodies.
The Relays also have their own on off switches. The Rachni War and First Contact War were both started due to species activating the Relays without thinking what could be on the other side. All Relays work in pairs. Even the multi point secondary ones need to pair with another relay to travel to it. Manually shutting them down which the Reapers should be capable of since you know they made them. And made them with the intent for them to go into shut down mode and reactivated each cycle. The entire logic of the Rachni War and Krogan Rebellion also makes no sense if the Citadel could control the Relays. Shutting off 1 Relay remotely would have ended the Rachni War before it began. Krogans would have been locked in solar systems with no way to reach other races to do damage.
The Citadel controlling the Relays and the 1 instance it actually showing any power to do so makes no sense the same way you tend to argue the existence of the AI on the Citadel makes no sense. There is one application of it right at the end of ME1. And only then to try and justify why the instant the Citadel was attacked the entire Council races didn't jump to defend it instantly. I suspect in ME1 there was probably a larger plot point about the Citadel and Relay control that was dropped or removed leaving only the singular line from Vigil. Just like there was probably a plot point that explains why Liea didn't hug Chewie at the end despite what happened going for instead the brand new never seen before girl.
Sovereign didn't need protection. The Geth fleet was already in existence and was chewing apart the Citadel fleet. According to the game all the relays around the Citadel were locked. So WTF did he need protection from? And even afterwards he sat still and they couldn't damage him. The only reason Sovereign is destroyed even after getting the entirety of the 5th Fleet from humans to show up was because of plot device overload from Shepard killing his robo puppet.





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