OK, lots of good points from a lot of people. I'll try and add my thoughts in quickly.
I agree with you up to a point. I think the writers wanted us to think Shep was experiencing outside influences before The Choice. The woozy focus and whispering voices point to that, although somebody here posted that was leftover from an abandoned story line of TIM developing a way to indoctrinate people. I don't know. I do think it was added to the end to heighten the drama
You lost me here. I used to be a Destroy guy but after replaying and hearing those conversations with the crew and Garrus, I'm turning into a Control guy. I'm convinced that a big part of ME is about learning to seeing the Geth as living beings. In order for a Catalyst Choice to allow the Geth to survive, the blue/control choice has to be the paragon choice.
I didn't see the Star Kid full of nonsense and non sequiturs. Care to elaborate?
I decided to be mildly humorous rather than writing a dissertation. I'm still going to try and be brief, but basically saying something like "if a fire burns is it at war?" does not equate to sufficient rationale to destroy known civilization across the galaxy. That is bonkers. That is, maybe, at best a B- in a freshman philosophy course, not the overwhelmingly logical reasoning of a supposedly unknowable infinitely intelligent AI. Reasonable adults shouldn't be swayed by that sort of shallow argument. The only response necessary to refute that sort of things is, "dude, you're not a fire." End of conversation.
An artificial construct saying that the created will always try to surpass their creators, and therefore need to be stopped, while it attempts to surpass everyone by dictating the fate of the galaxy is an inherent contradiction.
Star Kid attempts to side step that contradict with another idiot-savant one liner of "I'm just an AI, the same way you're just an animal" to which any sensible person would reply, "yup, I am just an animal - glad we agree, now you're still full of shenanigans and you're a crazy AI who wants to do everything you're saying you're trying to stop."
Vendetta also detects Indoctrinated forces, in Kai Leng, but registers absolutely no influence over Shepard or the crew at any point
This is a big point. A lot of astute folks have brought up something or another about indoctrination, what it means, what counts as indoctrination, whether or when Shepard was potentially indoctrinated, etc.
To elaborate, I don't think Shepard was indoctrinated per se. I think what happened is that the "rapid indoctrination" or the super indoctrination (my term) failed to work when TIM was controlling Shepard. Shepard basically broke the strongest indoctrination attempt possible, likely because he's basically half prothean half human (due to the cipher). The only other person to have beacon contact and the cipher was Saren, and ultimately he does break indoctrination long enough to shoot himself (which if you read Retribution and see what happens to Grayson, you know this should be almost impossible). The half prothean half human wrinkle maybe makes it hard for Reapers to figure out indoctrination perfectly because the brain is operating differently at that point.
Anyway, having broken the strongest form of indoctrination, the Catalyst realizes it has to essentially trick Shepard, since it can't dominate him.
Wait... are you saying you missed the blatantly obvious parallel to Cerberus there?
Nope, my post was just getting long, and I'm a sucker for brevity. It's the writer in me. So I thought I'd skip the obvious, "Cerberus and TIM prove control option is... etc, etc". But as another person said, the Cebrerus/TIM/Control angle was clearly right there. It's part of what I'm saying in that you're clearly meant to have doubts, but somehow people took that into this whole dream sequence, "BW intentionally told us a false story to be clever", which I think takes it too far.
Also: (mostly) all of you are really smart people, and I like this forum a lot.