The video explains this. Shepard 'wins' against the indoctrinated part of his mind no matter what you choose (except for that one choice that gets you a CMF), and because of that he lets go of his willpower (Anderson dying), leaving him completely open to suggestion (in StarChild, and why he is so quick to agree to everything StarChild says).
Except, and I'm watching the video right now, Shepard is the willpower, not Anderson.
"Anderson speaks to Shepard, not the Illusive Man. The resisting mind tries to make the will aware of the indoctrination attempt."
So, when Anderson dies, Shepard isn't losing his will, he's losing his resisting mind. And with TIM dead, he's losing his indoctrinated mind. So all that is left of Shepard should be his willpower.
So if that's true, shouldn't Shepard be less impressionable when heading up to the Catalyst?
--
TheRock ~ Slow dramatic zoom-pan. Doesn't phase the hooded man.
"You have issues." - MWC. Pot. Kettle.