The only reason you don't believe indoctrination took place is because you have suspended your critical thinking skills in favor of accepting an illogical premise because it gives you a warm fuzzy feeling.
The Twilight God wrote...
So of course a typical argument against any indoctrination theory is, "But the Extended Cut disproves anything and everything involving indoctrination. Everything turns out great. In fact, things turn out better in the Control and Synthesis endings than they do in Destroy. All Praise the Reapers for their truth and honesty!”
But do things turn out better in Control and Synthesis?
This is never definitively elaborated upon. All of the epilogue slides involve a narrator speaking about what they foresee will happen, want to happen, hope will happen or plan to make happen. The slides do not actually occur in real-time. Nothing in the slides actually occur in-game. The endings don't happen in the future. The endings are in the present. No time travel takes place. The EC slides are intended to placate angry fans by showing them pretty pictures. Ignore the slides and just listen to what the narrator actually says. The narrator does not describe what is on screen. The narrator cannot know if any of that stuff would happen as the narrator is speaking from the perspective of a person in the present. It is merely an individual talking about their hopes for the future in a general manner. No direct mention of krogan babies, geth-quarian peace, Jack becoming the headmaster of Grissom, Miranda becoming president of Earth, or anything else of that sort. Bioware counts on people to see what they want to see. Many players assume everything in the slides is an actual depiction of the future. There is no evidence of this being true. There cannot be as the endings take place int he present.
Even the Stargazer scene, which takes place in an unspecified place and time, involving an unspecified species is ambiguous. The Stargazer says, "Some of the details have been lost in time. It all happened so very long ago", so for all we know whatever ending the player chooses is just his telling of the legend. Even if the player chooses Control or Synthesis, Destroy can still be what actually occurred "so very long ago". Also, we don't know what occurred between the end of ME3 and the Stargazer scene. It's possible the galaxy, in another cycle, had to battle the "Shreapards" or there was a guerilla war to break free from synthesis indoctrination (Matrix style).
Another argument is the blurb which pops up after every ending states "Congratulations on bringing an end to the Reaper threat..." First, this is something that exists outside the game itself. It's in the same category as the main screen where you pick New Game, Load Game, etc. Second, it says the same thing after the Refuse ending in which nothing Shepard nor the player does brings an end to the Reaper threat.
Control
The only thing we know occurs in real-time regarding the Reapers is that they cease their immediate attack and begin repairs on the relays. The narrator is speaking about what they will do; Not what has been done. The epilogue may be narrated by a Shepard flavored Starbinger whose goals are identical to its predecessor. When it says it will give the many hope and a voice in their future, when it says it will protect the many, it could very well mean ascending them into reaper form to protect them from being forever lost in a hypothetical synthetic ushered apocalypse. Or it could be a delusional Shepard within the great Reaper super consciousness deceived into believing it is in control. And although it has a positive outlook for the future, none of it ever comes to pass.
During the conversation on the Citadel with The Illusive Man, Shepard can say, "Then open the arms, let the Crucible dock, and use it to end this."
The Illusive Man 's reply to this is, "I... I will."
The entire narration by the Shepard AI in the epilogue amounts to "I will do this and that", not "I have done this and that".
Shepard then goads The Illusive man shouting, "Do it!"
The Illusive Man reacts by saying, " I... know it will work."
Shepard continues to taunt him with, "You can't can you? They won't let you do it."
The Illusive Man protests, "No, I'm in control. No one is telling me what to do."
The Shepard AI is convinced that it is in control.
The Illusive Man continues his protests, "No. No! The two of you, so self-righteous. Do you think power like this comes easy? There are sacrifices..."
Apparently, Control supporters think it is easy.
Shepard: You sacrificed too much.
TIM: Shepard: I... I only wanted to protect humanity. The Crucible can control them. I know it can. I just...
Yes, and the Shepard AI also wants to protect humanity. But can it?
Imagine if an ending to Mass Effect 3 was The Illusive Man shooting Anderson and Shepard dead followed by a near identical narration to the Shepard AI. Just substitute The Illusive Man's voice for Shepard's voice. How confident would you be that the galaxy was truly safe? So why should we be sure that the galaxy is any better or worse under Shepard, who has an astonishing change in opinion on Control five minutes after opposing it? Factor in his use of a reaper device that makes no sense functioning as advertised. It has been established in Part II of this thesis that there is no reason whatsoever for the Reapers to construct a device that relinquishes their ability to pursue their intended goals. There is simply no way anything good can come of Control. It is a narrative and thematic nigh impossibility. Any cease-fire can only have been temporary. The Reapers would inevitably continue the harvest once the relay network was reestablished. Given the power of their forces such an interlude isn't detrimental to them and with the Citadel firmly in their control resistance is all but eliminated. The relays could have simply been a higher priority. They had to be fixed at some point anyway and this way they have more manpower to repair them vs. waiting until after the fighting is concluded. The writers perpetuate the indoctrinated perspective on the player even after the credits have rolled.
Eternal. Infinite. Immortal.
The man I was used these words, but only now do I truly understand them.
Through his death, I was created. Through my birth, his thoughts are freed. They guide me now, give me reason, direction.
There is power in control. There is wisdom in harnessing the strengths of your enemy.
Here I'll end it with Shepard reiterating The Illusive Man's reaper induced views about controlling them. Not unsurprising that now he "understands" after his interaction with the reaper device. His "understanding" appears nothing more than the same erroneous self image we've seen before from the likes of Sovereign and Harbinger.
Created, and yet infinite? Simply multi-present and yet infinite? Immortal and yet killable? If he understands these words, why do they betray him?
Reapers are not infinite. Not individually or collectively. They have a beginning and they have all the time in the universe to find an end. Ask Sovereign. It made the same assumption about itself before it was destroyed.
Synthesis
"My mind is still my own... for now. But the transformation from ally to servant can be subtle."
"Sovereign's manipulating you and you don't even know it! You're already under its power!"
The epilogue slides are narrated by a reaper influenced EDI whose perceives the galaxy in the way the Reapers desire her to. Like the Control narrator, EDI speaks in terms of what will be; not what is. EDI seems sure that peace will reign across the galaxy in a grand utopia. Dr. Kenson also envisioned this Reaper ushered utopia while she was indoctrinated. Saren envisioned a grand destiny for organics brought on by synthesis while under the influence of indoctrination. How does EDI arrive at this conclusion if everyone's free will remains intact? Why would she assume anything will be different if no one has been fundamentally changed psychologically? She has to know something we don't, consciously or otherwise.
I conclude that free will as we know it, the "petty freedoms" that Saren points out, are removed from the equation. This can be taken as a good or bad thing. One could argue that we never had free will. We act and react according to chemistry. Mother Nature dictates our motivations and the illusion of choice is merely our predisposition to identify with the will of nature. Instead of maintaining conscious objectivity and knowing "this form requires chemical energy", we are identified with the natural world and think, "I am hungry". But in nature there is the survival of the fittest. Traits designed to make us successful in a dog eat dog world. There is fear, selfishness and anger. These are things which result in conflict and suffering. Instead of mother nature to guide our supposed free will the Reapers guide it in a way that is more appropriate for our level of advancement. Synthesis is therefore not an abrogation of free will. As there was never any genuine free will to begin with. Synthesis is therefore the replacement of an outdated pre-industrial psychology for a newer, more appropriate, psychology for the modern age. You will still have people who are certain that they are special and different than every other creature in the natural order. They will insist they do, in fact, possess genuine free will and will view the Reaper modifications as an abrogation of their supposed right to self-determinate. Ignorance is bliss. But some people will insist that ignorance is immoral. Ultimately, it is up to the player to decide if Synthesis is good or bad.
Of course, this all hinges on rather or not the cycle continues or the Reapers view the current situation as satisfactory. It has been established in Part III of this thesis that Synthesis is not the Reapers' ideal outcome. Is there a possibility that the Reapers will continue the cycle in a non-violent manner or work to reverse synthesis so that life, and the cycles, can continue as it was? Conceivably, yes, but there is nothing in the ending to substantiate the claim definitively. But it seems likely to me. For one, ALL life is synthesized. Therefore, evolution has been stifled throughout the entire galaxy. The cavemen of our day will forever be cavemen. The toad lizards of Omicron Persei 8 may never evolve into the space faring Omicronian race as their DNA is "perfected" in synthesis. Plants and beasts cease to adapt and change. The possible advent of immortality may result in a return to the cycles for the sake of population control. The only difference being that everyone agrees to become Reapers. That or all life is halted as is and no new life is ever allowed to come to fruition. Both are unappealing in my opinion. Where Control is definitely a continuation of the cycle, Synthesis is more vague in terms of exactly what happens next. Regardless, the writers perpetuate the indoctrinated perspective on the player even after the credits have rolled.
Overall, I would say that Destroy is Freedom, Synthesis is Enslavement and Control is Destruction. Refuse represents Defeatism which is the antithesis of the entire series.
Why deceive the player?
If Control and Synthesis ended like the Refusal Ending it would invalidate those endings for the majority of players. Refuse was only added because players requested the option (albeit with a different outcome in mind). The player must be allowed to believe in the endings or else everyone would simply reload and pick Destroy. It would defeat the effort put into making the endings. Shepard falling prey to indoctrination, although not the ideal conclusion, is still a narratively sound outcome. And in this way the writers keep those endings valid by having the epilogue continue from the indoctrinated perspective. Who would pick an indoctrinated ending otherwise? Not many.