But you werent even close to being indoctrinated at the asari world, you just had the early signs of being so in occasional nightmares. Ninja boy was indoctrinated.
We see several indoctrinated characters in the series. Some of them seem to act normally except that they're working toward the reapers' ends, and some are little more than zombies. But the fact is, we never see indoctrination from the perspective of the victim, nor is it really clear what goes on in their heads, so we don't know what it would look like.
From the codex entry on indoctrination:
Organics undergoing indoctrination may complain of headaches and buzzing or ringing in their ears.
These are all so vaguely worded that you could attribute anything to them. I have stress-related headaches and tinnitus, I must be getting indoctrinated!
As time passes, they have feelings of "being watched" and hallucinations of "ghostly" presences.
As far as I remember, Shepard never had feelings of being watched or hallucinations of ghostly presences, unless you think a completely ordinary-looking kid as being "ghostly". And please don't say "but the dreams", as hallucinations are by definition not dreams.
A Reaper's "suggestions" can manipulate victims into betraying friends, trusting enemies, or viewing the Reaper itself with superstitious awe.
Shepard never did any of this, that we saw. You can argue unreliable narrator all you want, but if we're going that route I could make a much more convincing argument that Shepard was injured when he was buried under rubble at the end of the first game and the entire rest of the series was just his coma dreams. Hey, it explains away pretty much all the plot holes in the series, so it's obviously it must be true!
Beyond that, every case of indoctrination we saw in the series occurred with people who were in reapers or near reaper artifacts. Shepard wasn't near a reaper long enough to actually be indoctrinated any time during ME3. Unless you think someone can be partially indoctrinated and then set loose for the process to finish on its own, but not only is there no evidence of that whatsoever, it also directly contradicts how indoctrination is described to actually work.
As i said, the lead writter had complete and total creative freedom, they didnt even knew what the ending was going to be like at release, they didnt care, the dude made them tons of money and they trusted him.
You're not making any sense. The lead writer had complete creative freedom, so they wouldn't let him do the game with the IT as the plot? Or did the other writers want to do the IT and the lead writer came in and stopped them? I think it's pretty naive to assume that the higher-ups wouldn't be aware of what the game's plot was at every stage of development. EA isn't exactly famous for their hands off style of management when it comes to a game's content.
I still don't buy your reasoning about changing the game's plot based on legal fears, by the way. Not only is there no real world evidence the game's plot was changed from the indoctrination theory to something else, but there's no evidence EA ever had legal concerns about ME3's content, or that Bioware was ever considering trying to release a 4th mass effect game continuing the story. Your entire reasoning for the plot to be changed is nothing but pure conjecture, not supported by any real world facts and built around the myriad of inconsistencies and plot holes ME3 is littered with because it's a half-finished half-assed game made by hacks with delusions of grandeur.
And that's why the indoctrination theory is bullshit.
