ReggarBlane wrote...
Indoc theory is based completely on the rushed, sloppy part of the ending.
Pointing out rushed and sloppy work as proof forgets that rushed and sloppy work lacks intent to create the situation.
There's plenty of other instances throughout all three games suggestive of the theory. It's not just a reaction to the end. I even questioned Shepard's sanity through the second game and thought to myself her mind had to have been affected to some degree by the Reapers.
There are missions and scenes where she hears voices and she's been inside a derelict Reaper, handled Reaper technology (remember it was said that even the smallest Reaper tech could invade your mind) and been exposed to Prothean beacons that, for all we know, could make her more susceptible to Reaper indoctrination.
Stress expends a heavy tax on the mind, how hard would it be for the Reapers to slip in a subtle indoctrination? Also recall Saren's expletive: "my mind is my own, for now." Refer to this:
http://masseffect.wi.../IndoctrinationRead that and carefully dissect the implications therein. Cybernetic implants make it easier for the Reapers to control organics. The synthesis ended has all organics synthesised in a way and the Reapers still live. Wouldn't it then just be easier for the Reapers to assume direct control of every synthesised being? Thereby enslaving the entire galaxy. They could just take what they need from each race, destroy the rest and wait another 50,000 cycles for it to begin all over again. Even if they become part-organic themselves how does that change their mind-set? Each Reaper is an independent AI and Harbinger and Sovereign particularly exhibited signs of sadism and a superiority complex.
By "destroying" the Reapers Shepard is being counter-intuitive to the Starchild's rationalising and in this sense is logical to weakening indoctrination. By opposing the suggestion that the Reapers
not be destroyed through synthesis (the supreme solution) or control (which an
indoctrinated Illusive Man wanted), Shepard is countering what the Reapers actually want.
They were so close to the Crucible when Harbinger swooped in and blasted everyone in London; they - the Reapers - could have feared Shepard might actually accomplish her goals and had to intervene, knocking her unconscious with a near-miss and attacking her mind at its weakest.
I could go on why I advocate IT but that might bore you

I just think there's strong grounds established by previous games to support the theory.