Actually, Indoctrination can when strong enough. When Shepard tells Saren to stop, the Turian can't. Another explanation is that Indoctrination makes the victim more susceptible to Reaper commands. Sovereign probably never said anything about Saren not offing himself. Also, we never hear Saren muttering something about a little boy Turian offering him enigmatic choices.
Besides no other Indoctrinated individual has ever experienced Shepard's flavor of Indoctrination. They emit energy waves that damage the brain, we've never seen illusion trickery. No one has ever even seen the kind of hallucinations Shepard is allegedly seeing. Also, Vendetta's Indoctrination detecting protocols never detect the taint of Indoctrination in Shepard.
Another thing about IT while I'm at it. It has the premise that Shepard has some sort of set psyche and that deviating from that leads to Indoctrination. This is completely antithetical with Shepard's roll as a dull player insert that's been established throughout the trilogy. For the choices, the justification for whatever solution Shepard makes is established by the player. Whatever metaphysical/symbolic whatever for why Control and Synthesis is highly subjective.
Also, what is the deal with the low EMS ending variants? Why does the Collector Base decision mean anything for why either only Control or Destroy are options? Like all the solutions the justifications for keeping or destroying the base are highly subjective.
Maybe because they knew Shepard's eyes were synthetic? That having them erode like regular tissue would be a plot hole?
Shepard says there's still time, you can stop this, and Saren replies that he could be right, there might be a chance.. But then Sovereign halts him, so as his way of stopping things, he shoots himself in the head. So he almost pulled up the willpower to stop it, but Sovereign was too strong, likely because of the Reaper implants.
I'm not sure about the illusions, but I remember in ME2 where you were going after the Reaper IFF, there's a console with two engineers talking about how they have the same memory, so using memories is obviously something they can do and has been documented.
Vendetta didn't detect Shepard as indoctrinated at that point because has only undergoing indoctrination. "Organics underogoing indoctrination may complain of headaches and buzzing or ringing in their ears.". There were many times he was waking up with a headache or you hear strange sounds.
All three games Shepard has been talking about destroying the Reapers. At the last moment, you're telling me it's logical for him to switch his approach, just because some glowing AI that is in control of his major enemy tells him it'll work? But he'll have to die in the process? Really?
Low EMS choices just means they've had less chance to complete the indoctrination attempt, so they can't push their own agenda onto you because you're not susceptible enough. If you kept the Collector Base intact in ME2 then you agree with what the Illusive Man was saying, that you can learn from their tech and so on, so Control is your option of choice while under indoctrination. Destroy it and you still just want the Reapers gone, regardless, so Destroy is the only option.