I don't get IT.
Indoctrination Theory relies on the idea that Shepard is being indoctrinated during the final conversation with the Catalyst, and that if the Catalyst successfully persuades Shepard to pick either Control or Synthesis, the indoctrination attempt has been successful. (Some extreme versions include Destroy, with Refuse being the only unindoctrinated option.)
But... No.
Indoctrination doesn't work like that.
Consider our three main in-game examples of indoctrination. Saren, Kenson, and TIM. Consider what indoctrination meant for each of them. For what it's worth, for none of them did indoctrination mean agreeing with the Reapers.
Saren reached the conclusion that submission was preferable to extinction - failing to consider that submission might mean extinction and that resistance might be the only chance at survival.
Kenson reached the conclusion that the Reapers couldn't be a bad thing for the galaxy, since life continues after each cycle - failing to consider that simple continuity of life was meaningless in the face of the destruction of civilisation.
TIM - ah, TIM. He's probably the best example. TIM reached the conclusion that Control was preferable to Destroy, but completely failed to consider that Destroy was still preferable to a Reaper victory.
What do we see in common?
A failure to consider very simple perspectives.
What don't we see?
Any sign of a hallucinatory final test of their resolve before they become fully under the control of the Reapers.
They were never fully under the control of the Reapers (with the exception of Saren after he was already dead).
By my understanding, indoctrination acts as a form of mental tunnel vision. Every single thought that you have is still your own, but thoughts that align with the Reapers' goals are encouraged, and other thoughts merely become less likely. Both Saren and TIM were broken by forcing them to consider perspectives that the Reapers had blinded them to - but the goals that they had were still very much in character for they were. (TIM wanted ultimate power; Saren was actually trying to save organics.) Their free will was still intact - it had just been subverted.
I can't reconcile this with what is presented by Indoctrination Theory. IT tells me that, for picking Control, my Shepard wakes up a puppet of the Reapers, all free will gone. So, because I decided that I'd prefer to put galactic power in the hands of one man rather than wipe out the Geth, suddenly I'm fully indoctrinated?! I don't see how that perspective leads to me working for the Reapers. I cannot see the connection.
Is there a bunch of weird stuff that could be counted as evidence that something fishy is going on? Yes. I tend to ignore it, but yes, it's there if you want to see it. But "Shepard is bleeding from the same place as where he shot Anderson" is not evidence for "Control and Synthesis are indoctrination!". Neither is "Anderson got ahead of Shepard on the Citadel". Nor is "We've seen this kid before." It is evidence for "Something fishy might be going on" - nothing more, nothing less.
Is something fishy going on? Maybe. I can't discount it. Is it what IT presents? I doubt it - because as far as I can tell, the indoctrination presented by IT is nothing like indoctrination as we've seen it before.