The problem with having an "invert mouse y-axis" option is that you are using the mouse to move a pointer around on the screen (e.g. to click HUD elements or to target an enemy ship) at the exact same time you are using the mouse to "steer" the ship. If you actually did invert the mouse, it would probably be even more confusing for you than it is now.
Most people who have played the game have found the mouse system very intuitive as it is. Even those who normally invert the mouse when playing FPS games have said it is fine. Of course, there are always a few people whose brains can't easily let go of the control system they assimilated when playing another game. A few of them have reported motion sickness from having the controls work opposite to the way they expect.
Note: I am not denigrating those people, this is a genuine problem for them. I've seen similar reports from people who are used to airplane style joystick behavior trying to use a space combat sim like Freespace (or vice versa).
--milo
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