I know the subject of the eyes has been brought up a lot. But I've talked to quite a few people who don't see it, or don't think they're really what we think they are. So I got some screenshots and when necessary magnified them so you can see them better.
That's the Illusive Man's eye in ME2. Note the pattern: an inner circle, an outer circle, and two orb shapes on the bottom left and right.
This is Saren's eye in ME1 right before he ragequits existence. It's different, but similar in a way. A large glowing center, an inner ring, a much smaller outer ring, and some wavy designs coming out of them.
This is Shepard's eye right after his face turned black in the control ending. This is the exact same pattern as the Illusive Man's. The only difference is the color. Which is similar to Saren's. I'll also note that the rest of the scene he seemed to be in immense pain as he's gripping the handles. After he turns like this, he simply looks deadpan and emotionless.
This is Shepard's eye during the synthesis ending. He's further from the camera and a lot of the time it's distorted by the green pulses, but this is still a clear enough shot to tell, without a doubt, that he has the same eyes here as in control.
Hopefully this helps convince someone that doesn't believe the eye evidence, which I personally consider to be the strongest evidence of the indoctrination theory.