Indocrination: A hypothesis stitched together with weak threads and cherry picked examples. Glenn Beck would be proud.
First, I would like to apologize if my points here have been covered. I'm not reading 45 pages to get the whole conversation. I have a job and stuff.
Why does it matter that the destroy option is red? My character was a sociopathic cadaver-junky. Most of my rep points were renegade. Why didn't the Catalyst, being all up inside my mind and dicking with my subconscious, change the colors to manipulate my personality type? Why wouldn't it make the synthesis option red for me, since I'll click on any renegade option? You're assuming, like everyone else who plays with some sickly good paragon character on their first play-through, that the paragon options are the default, or even most rational decision to make in any given situation. This point only reflects your gameplay bias and is inadmissible as evidence.
A transforming space station doesn't itself indicate a dream or illusion. This is a sci-fi story, and the main enemies are Lovecraftian machinations that sleep in "dark space" for 50,000 years. Shifting walls isn't so hard to believe, and remember that in ME2, Anderson noted how amazingly fast the Citadel was being put back together. Restructuring itself is obviously not such a difficult task. Likewise, Anderson no doubt heard about Shepard's description of the Collector base. The Collectors, using Reaper technology and being trained by the Reapers to harvest organic life, will undoubtably make their surroundings look the inside of a Reaper base (which, as it turns out, the Citadel is). The radio chatter you hear can be chalked up to no one being able to count the casualties. While the ending is vague enough that your interpretation is possible, they are not themselves sufficient to conclude that Shep was delusional, dreaming or indoctrinated.
Conversations with Anderson, TIM and Hackett can have many interpretations. That they lend credibility to the indoctrination hypothesis is non-sequitur. Your interpretation of the boy's significance is outright impossible. What was clear to me through the game (though arguable itself, I suppose) was that the boy represented Shep's anxiety about not being able to save everyone. The dream sequences would feature more and more of his fallen friends' voices, as well as the shadows of countless deaths he has had to cause to win the war. This theme is repeated throughout the whole series, but the loss of the boy he couldn't save on Earth clearly had an emotional impact on Shep. The dreams were about his fear of not being able to fulfill his duty to protect the galaxy. Your interpretation, that Shep's subconscious was somehow aware of the boy's role in the future, opens even more plot holes than it closes. Why did the Catalyst choose that particular form for Shep, especially if his subconscious has been telling him that "no matter what happens you will get burned by trusting the kid" [OP]? I mean, it seems like the most counterproductive form to take, if the Catalyst wanted to manipulate Shep. And how does Shep's subconscious know to not trust the boy? What did the boy do to deserve this mistrust? Order the Reaper to shoot down his shuttle? Unless you have a lot of subtext from the game to back your assertion up, the subconscious angle is abject lunacy.
And so the whole house of cards that is the "Indoctrination hypothesis" falls down. Now, it may be that Bioware comes out later and says, "Yeah, that's totally right. Shepard was indoctrinated alright", but that would be a cop-out. There is nothing in the story that should lead anyone to such a conclusion. The ending simply doesn't make any sense, not one bit of it. Given this, Occam's Razor dictates that the reason for the ending sucking so bad isn't a complicated or hard to justify dream sequence, but poor decisions from the company. Bioware failed its customers, plain and simple. They are either too outright incompetent to finish the story, or they feel they have some crafty business scheme in delaying a non-ridiculous ending, which makes them terrible story-tellers.
This whole thing is silly.