Gethsemani said:
I'd almost agree with you. But there are a few things to keep in mind here:
1. The "growl" is mentioned in one of the novels as a side effect of breaking through indoctrination.
Not having read the novels I'll defer to more experienced people on that one who has read them, but I'd like a novel quote on that if you can provide, because it got me curious. I might actually have to read them now

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Gethsemani said:
2. Shephard suffers from vivid nightmares (complete with Reaper growls) throughout the game, which is another sign of indoctrination. This is mentioned by the Cerberus scientists in the derelict reaper as occuring during initial indoctrination.
The Reaper Growls in the Nightmares have nothing to do with indoctrination. They appear when Shephard is close to the boy, making the boy run, symbolizing him trying to escape from them, and then he always flees further away afterwards (making you once again run to catch the little Son of a b****).
You are right that nightmares are mentioned as something the scientists experience as an indoctrination sign, but that alone isn't a very strong indicator. As for your last part:
Gethsemani said:
3. Lots of conversations with Hackett, Anderson and the crew, especially during the first half of ME3, is Shephard wondering if she actually has what it takes to facedown and defeat the entire reaper armada.
...two important things to point out:
1) A lot of that can actually be changed by what you select in conversations. The player has a lot of influence on Shephard in that aspect, and there are many times where you have the option to decide to make Shephard appear as if the war is affecting him (or her) more than it seems, or to keep up the iron-will. The choice is free.
2) It doesn't change the fact that Shephard does NOT give up. Wondering whether or not it's possible to defeat the Reapers is not sign of indoctrination, given that they are indeed an overwhelming and 'overpowered' enemy. Having inclinations towards giving up (or searching for alternative solutions that doesn't work, like what Saren did, or the Illusive Man trying to control them) is a sign. Shephard might do the former (again, depending on your choice in conversations most of the time), but not the latter. He/she never has any inclinations towards giving up, only ever admitting that it was never gonna be an easy fight.
So once again, Shephard is still determined to do what he or she always had set out to do. Indoctrination would have changed that. In fact, if Shephard we're indoctrinated we likely wouldn't be playing the game, because the Reapers would be directing the show. I very much doubt the reapers would willingly let their indoctrinated servant take out two of their destroyers directly (three if you count the one on Tuchanka as well that was killed by Kalros), cure the genophage, destroy their Rachni breeding ground and i could go on about Shephard makes life annoying for the Reapers.
Gethsemani said:
It is also worth noting that the indoctrination part of the codex suggests that it is possible to "instant indoctrinate", which might be what Harbinger did to Shephard during the endgame.
No it doesn't. That point of the codex is actually refined during Mass Effect 1 in regards to how Saren was indoctrinated versus all the test subjects on his research facilities. Rapid indoctrination is not "instant". It's much faster than normal indoctrination, which takes a couple of weeks (a 1-2 week estimate or so), but we are at the very least still talking a few days.
Also, rapid indoctrination severely hampers mental functions, leaving the victim an unintelligent being very fast with hardly any intelligent brain functions (for example, the victim would likely be unable to speak anymore, maybe mumble at best). Shephard doesn't experience that.
Equally important, i find it ironic that the supporters of the Shephard Indoctrination theory can't seem to agree on this point. Notice how even you brought up two different versions in your post alone: The one that has Shephard indoctrinated through the entire game, and the one that has Shephard being 'instantly' indoctrinated by Harbinger during a run for the beam. If it's the instant indoctrination version, then the dreams during the game aren't a supporting argument. People just can't make up their mind

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Gethsemani said:
After all, at that point Harbinger doesn't want Shephard as his puppet, he just wants to prevent Shephard from actually succeeding, and as such doesn't care if Shephard is reduced to a gibbering shell of a human within hours.
And this is another point I've made: Why not just kill Shephard then?
Harbinger is there, shooting everything around Shephard with a big fat red laser. Even assuming he could instantly indoctrinate Shephard (with or without resulting massive brain damage), there is no motivation for it, so why bother? To them, Shephard is just an organic that happened to have a little bit of 'luck' along the way, but is meant for destruction or harvesting regardless.
And if Harbinger actually HAD the ability to indoctrinate instantly over distance that way, why haven't they done that with all the human forces while Shephard was out there flying the galaxy thin? Why not eliminate most resistance that way and get the resistance to surrender through indoctrination?
Occam's Razor.
Gethsemani said:
EDIT: Let me point out that I am not necessarily supporting the indoctrination theory, I am just saying that if they decide to go this way and retcon the ending, Bioware has left themselves some wriggle room.
On that we can agree. The more 'uncertainties' you leave in a story, the more wiggle room you have later.
But let me let you in on a little secret: the people who support this theory only do so because it's something they as the fanbase themselves came up with, thinking 'Ah, we got you figured out BioWare'. So basically, they consider the theory better than the actual ending because they consider it their own idea.
However, if BioWare had come out during the ending (after all the bullshit we got) and had revealed Shephard to be indoctrinated throughout the entire game and that most of what players think they accomplished in the game were actually just Shephard dreaming, then they would be raging on BioWare for that shit ending for the simple reason that it suddenly isn't their idea anymore, and then they would actually realize that the indoctrination theory pisses as much on players as the actual ending did and are just as bad (if not worse). Ironic isn't it?

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