Less than a year ago I did a flight in a 172 as a rear passenger and it was the first time I felt headaches and discomforts. Does anyone else here feels like it? I got to say, as a commercial pilot and flight instructor, seeing the pilot not doing a great job handling the plane without the ability to do anything about it, also scared me a bit (so much so I'd had to rate his landing a 2, potentially even a 1, if it was a pre flight test eval)
So there are two issues here.
The first is the headaches and discomforts which I agree with the above posts, although my experience with training aircraft is well behind me and so I defer any expert opinion to those with more current experience.
The second is the pilot handling issue you identify. As an instructor or check pilot you have to look at how outside influences affect your grading. Is it possible that the headaches you felt were causing you to grade harder than you normally would? Is it possible that your inability to control the situation led to your harder grading? Is it possible the same root cause that was causing you discomfort was also causing the pilot flying similar discomfort, and that is what led to the poor handling? We're all human, and it's entirely possible that your headaches and discomfort along with your inability to control the situation caused you to evaluate this pilot differently than you might otherwise would have had you not been in pain or had you been in a position to take the controls...or not, maybe this pilot was handling the aircraft poorly, but the way you wrote the two sentences gives me a moment of pause.