Ok, for example... I'm stopped in a mech, in a slope, and I'm looking forward. My torso is turned 180 degrees and I turn my legs to match it, leaving my torso pointing in the same direction (I actually move my mouse in the opposite direction my legs are turning).
At some point in the turn, the "eyes" (or camera, call it what you want) of my pilot look at the floor of the cockpit for a second or two... I would expect them to keep looking through the glass of the cockpit...
Basically, my mouse was pointing one way (thus controlling where I look) and the cockpit got tilted upward to a point where the point I was looking at before becomes the floor of the cockpit... (is it clearer?).
Think if you are in a mech yourself (virtually speaking) and your eyes are looking forward through the glass. If your cockpit suddenly tilts upward by a lot, are you going to look at the floor as if your eyes were fixed to a specific spot in space or will they follow your body's movement? The answer is they will follow your body's movement at least a little and then adjust to follow whatever object you were looking at before... I think it should do the same in the game...
Basically, have a certain deadzone where your eyes can track an object (by keeping your mouse aligned on it) despite the smooth "bobbing"effect, but that if the cockpit moves too much outside of that deadzone or moves too suddenly (i.e. after getting hit by a projectile) that your eyes follow that movement instead of staying fixed at the object you were pointing at before... The eyes of the pilot should always move relatively to the cockpit the pilot is sitting in in proportion to the movement angle and speed (i.e. small and slow = don't move, small and fast = move a little, large and slow = move a little, large and fast = move a lot...).
It's hard to explain what I mean... but I hope you get it...
If someone else understands what I mean and can explain it better, feel free to jump in!