See, I felt the idea of forshadowing indoctrination was there all along.
Mass Effect 1: Not much going on here, and any time you deal with a Reaper, you're with squandmates. But you're introducted to the theory. Shepard also demonstrates an ability to interface with Prothean technology, which impresses Liara. I mean, you're brain is rearranged now. You've picked up an extincted language.
Mass Effect 2: Reaper technology is used to rebuild you, including implants that alter your appearence, exposure to a Reaper ship that drove everyone nuts, Overlord where you interface with technology, Arrival where you're sitting next to Reaper tech and assume control of a mech. The implants and Arrival are the big deals because those do not involve your squandmates, which would explain why Tali and Garrus, present in all three games, isn't going insane.
Mass Effect 3: I think we've discussed a lot of things going on already in this tread, so I won't repeat it. But I would like to point out that during Shepard's waking hours, everyone is bugging Shepard on he mental condition. "Are you okay?" "Let's look at your implants." "Anderson is worried about you." Also, you have that asari from the first game that you spared...she also goes nuts.
I guess what I'm trying to say is that no matter how you play the game, or if you download the DLC...there are so many things that 'stack' against a sane Shepard.
Does anyone else feel like TIM pulled out Shepard's body, gave him/her a ton of mechanical enhancements without consent, just to deliever a new Saren for Harbinger?