"Indoc hypothesis supporters don't seem to understand that, especially in literary theories, one needs positive evidence to support their assertions. Speculations are not answers."
True enough, but I don't think everything is negative evidence. Sure, it fills plotholes, but there also appear to be deliberate artistic choices meant to convey Indoctrination, or at least a dream state rather than true reality. The dreamlike movement, being able to take down a marauder with two shots instead of the usual five clips or so, Shepard noticing an inconsistency when she notes that she can't see Anderson and he comes up with a response that seems a bit pat, the lack of a helmet when the citatel arms are open, the devil and angel on the shoulder nature of TIM and Anderson's arguments toward Shepard, graphical elements like dark tendrils at the edge of the screen, Shepard receiving the same wound Aderson receives, Space-boy's very appearance, since he appeared in actual dreams beforehand. These are all positive evidences, not "that explains away a plot hole." There are other possible explanations, but that hardly qualifies as negative evidence. WHY those elements were used in the way they were is speculation, but the elements themselves are evidence, and my human experience tells me that it would be near impossible to include so many elements that go along with the stated characteristics of indoctrination in a tightly-packed sequence without a deliberate attempt to do so. That last part is speculation, too, but it's based on experience and hopefully rational logic.
In the end, it doesn't matter whether you buy into the theory or not. The point of this thread was that the VI didn't catch Shepard's idoctrination and that definitively proves that the indoc theory is flat out wrong and those who believe it are stupid. THAT is indeed the use of negative evidence to attempt to prove a point. There is plenty of positive evidence. It's not definitive, and it never will be until we get a definitive answer from Bioware about what the whole sequence was about. But to say there is no positive evidence is, I think, absurd.
BTW, sorry for all the pontification. I just sometime like to get involved in these discussions. It's fun.