So I just want to throw some points into the ring to keep the theories flowing, because I honestly this theory is correct, so here's just a few ideas to spitball with.
1) When the Catalyst speaks to Shepard, there is an echoey feel coming from both of them as they talk. The difference is that when the Catalyst speaks, if you listen close enough, you can notice that the voice is entirely different, and sounds almost like a whisper. The one recurring piece of indoctrination throughout the series are the "whispers" in people's head as they slowly turn.
2) The only time Shepard ever saw the vent kid was in his dreams. Why is this situation any different? Why in the world would the Catalyst manifest itself as the kid. The only way the Catalyst would know to take that form was if it was in Shepard's head to begin with, as Shepard had not even mentioned the kid after his death.
3) Harbinger never once says he wants Shepard dead. Seriously, go through 2 and the closest he ever gets is "These attacks will tear you apart". If anything, Harbinger was making orders to keep Shepard alive. Most of his orders are more aligned with "Save Shepard, kill the rest." This kind of goes with the Harbinger wants Shepard indoctrinated theory. If you think about it, it is sort of weird how badly the Reapers want Shepard's body instead of just Shepard being dead. Even after he was killed, they were doing everything to retrieve his body.While it might be because they didn't want Cerberus to resurrect him, if that were the case, then why did the still want to take Shepard alive?
4) In the first game, there were small mentioning of Reapers using sleeper agents. If you truly think about it, you only really see one character who can truly be seen as a sleeper: Saren. All the others who served the Reapers, Collecters, Geth, and so on, weren't truly acting as sleepers as much as being slaves or worshipping them. Complete longshot, I know, but what if Shepard was among those sleepers? What if that is why the Reapers need Shepard so badly? If the whole point of the Reapers is to stop synthetics from wiping out organics, what better test is there to see if a generation can co-mingle, than the Crucible? I know this theory is shoddy at best, but it was just a thought.
5) The old man afterwards says that there's more stories to tell of "The Shepard". Probably just Bioware foreshadowing DLC, but still makes you think a bit.
6) One of the points that was brought up was how strikingly similar the ending of 3 resembles the ending of 1. If Bioware was going for the indoctrination/ hallucination ending, than they really would be planning to go all out with it. I got to thinking how strongly they are for story, and I remember how they almost punished players if they got their Shepard killed in 2. How they made it so in order to keep your character and to even keep the canon, you would have to go back to the beginning to try again. For Bioware to make a test like this, where if you break the story by doing something completely un Shepard your character dies, wouldn't be to out of their style. For them to release DLC that shows the true end of the fight with Shepard, but the only way to access it was with getting your Shepard out alive........ really does seem like something they would do.
All in all, I really hope that we're right. Bioware would become Gods amongst men if they did something as badass as this.