^ Still, the case could be made that these dreams are a symptom of latent indoctrination. Considering, for example, that every single time Shepard has these dreams is immediately after being in very close proximity to a Reaper (First on Earth, where the reapers are everywhere, then on Tuchanka where the damn thing almost steps on him at least twice, and finally at Kronos Station, where he has to climb the spine of the proto-reaper to get to the lab).
I would even go so far as to say that the original boy was always
a figment of Shepard's imagination; he saw him playing on the rooftop and later hallucinated him during the escape sequence as reaper nanides began to infiltrate his brain.
I know there are issues with indoctrination theory, but this single idea is the only thing I've ever seen that explains how the Illusive Man is able to control Shepard and Anderson in the end. He can control them -- to a limited degree -- because the REAPERS can control them, because they're both suffering early-onset indoctrination from being in the presence of the reapers for too long.