Really didn't understand all the confusion for ME3. Felt like most of it made sense, just a tad vague and stupid at times.
Regarding the indoctrination theory with the little boy: In the beginning of the game, other people do see the kid. When they are trying to escape on the ship, you see one of the soldiers rush the kid onto the shuttle. Of course your other teammates didn't see him, because they weren't there at the time.