My take on Indoctrination Theory.
Let me say this to start, Shepard is NOT immune to indoctrination. Yes, he has been surrounded in Reaper tech throughout the trilogy, but for some reason, he's never gotten indoctrinated. To be truly indoctrinated is to be under the Reapers' influence. Since Shepard is trying to turn those space squids into space dust, he can't be indoctrinated.
Now on to whats up with the Kid. The kid himself is just a illusion created by the Reapers to break down Shepard's strong will. But how can the Reapers influence Shepard like this if his will is so strong? Easy! Remember, Shepard's tried over this Reaper crap, he just wants to just sit, like Anderson at the end. His will is slowly weakening, thinking he may not win and that this would not end good. This leaves his will vulnerable enough to be influence if only a tiny bit, but it was just enough to show the manifestation of the child. Plus, don't forget that even if one doesn't act indoctrinated, a mass Apperance of Reapers like the assault of Earth will cause them to become indoctrinated ala the Asari from Saren's base. Because of this, Shepard was influenced enough to have that illusion of the child manifested. Because of this he begins his slow fall to indoctrination.
Reasons he loses will power:
•Years on the subject.
•Attack on Earth
•Death of the Child
•Worries of Earth and his people
•Fall of Palavaan(sp?)
•Situation of the Citadel-Refugees/Memorial
•Cerberus
•Injured Ashley/Kaiden
•Hearing about the fall of other planets
•Failing to protect Thessia/got his beat by Kai Leng.
•Reports that Earth is not good right now
•Dealing with Batarians over Alpha Relay
•Seeing Sanctuary
•Losing friends
•Dealing with old grudges between races.
•Learning the Reapers have taken the Citadel(lots of death?)
•Seeing Earth being overrun, "doesn't even look the same."
•The last push-Being attacked by Harbinger-Thinking he's gonna die.
Reasons his will is still strong:
•His friends and lovers
•The crucible
•A deep hope for a better future w/out reapers
After being hit by Harby, I believe everything that has came before about it being a fight to free your self. But in Illusive Man, controlling Shepard, yes. Controlling Anderson, no. Even if Shepard knows that TIM he has gotten implants, complete control over Anderson can't be possible for a mere human.
What happens next? No freaking clue. Maybe they go to Ilos, maybe they Actually enter the Earth conduit and blow the Reapers away. Who knows. Remember, this is all my opinion, but feel free to tear my post apart and speculate further.