Actually, I have another theory (and it is heavily backed on the ME novel)
Anyone who read "Mass Effect: Retribution" knows what I'm talking about.
(it tells about events that happens between me2 and me3)
In ME3 (game) there are small references to Paul Grayson and Cerberus experiences on indocrination (as far I can remember, these references appear when you are talking to Anderson about Kahlee Sanders and when you hit Sanctuary - the biotic academy and Kai Leng appears in the book as well).
During the first chapters, Cerberus uses Paul Grayson as a test subject for indocrination (probably he was the first attempt of Cerberus to better understand this process). After being "processed", the narrative says that Grayson fights against the "Reaper mind" trying to control him. He eventually succumbs and begins to fear that "they" [the reapers] start to read his memories (which actually happens later on). Although not in control of his body, he could see and experience everything the reapers were doing with him.
Ok. Based on this, I believe the boy that Shepard encounter during the attack on earth is REALLY a boy. After his death, he becomes a symbol of Shepard's inability of saving everything he fought for (this explains his nightmares).
In the end, when he uses the light beam to enter the Citadel I believe Shepard is somehow indocrinated (but he is in the very early stages of the process - Saren was indocrinated in a similar way). This becomes clear when the Illusive Man takes control of both Shepard and Anderson (although it's not clear how the control is seized... - TIM biotic powers or control over synthetic bodies) in the Catalyst inner chamber.
The ghost boy he sees after the Crucible's activation is actually an illusion the reaper's are creating into Shepard's mind (after reading his memories). Using the symbol of his fragility to make him act on their behalf. All endings appears to result in a bad scenario. Most people keep pointing that the "perfect ending" is the one that Shepard survives. But, according to my theory, this is the WORST scenario.. And why is that? If Shepard was being indocrinated and survived, the reapers achieved their objective and persisted in our hero's body.