I can see people can get very confused the first couple of times the game pauses automatically. As there is no prompt to tell you to press SPACE to pause/unpause.
The edge of screen panning doesn't play well with MMB for camera look and Panning Camera Breaks Focus, as you will hit the edge of screen with the mouse when using MMB, breaking focus and pan you wildly.
Perhaps lock the mouse cursor like when MMB for camera look is OFF, so it doesn't hit the edge?
The CONTROL options will take effect without pressing Apply. The graphical options, they will however keep the selection you have made without applying it. Example; you set texture to low, from high then press Esc to close menu.
You press Esc again and the selection is still on low, but texture in-game is still high and the Apply button is grayed out. So you have to cycle to medium, high then low. Now you can click apply and the game applies it correctly. (EDIT: The resolution also seems grayed out until you touch one of the other options first)
The ship's shaders and texture may bug out when you change texture size in-game. Maybe only let players change texture size from the main menu or let the apply be grayed out?
PS: I'm just finding these. I'm not saying they should be fixed, now or later, or how they are prioritized.