Try turning off mouse smoothing (pointer precision) under mouse settings, the mouse is a lot smoother and less jerkier without it.
Also try turning the mouse speed up when you play CC, it makes it easier to aim.
I attached an image to show where the settings are (control panel>mouse properties>Pointer Options)

Thanks for this - it pretty much solved all of my previous mouse issues.

Even with this fix for mouse acceleration, it still is there.
It's definitely in the game, so you can't completely make it go away by changing OS settings.

It worked for me, I guess it is just certain systems getting the problem.
Might be an incompatibility with certain drivers for different mice.

I'm not getting mouse acceleration anywhere except games where it can't be disabled. Logitech Setpoint can override the mouse settings of OS, but Cortex Command still has mouse acceleration.
I'm fairly sure it's in the game.

It's easiest to notice while playing in fullscreen. It's still present in windowed mode too, though.

Editing my mouse settings helps, but it does not come close to fixing the mouse in CC. It is effectively impossible to use the mouse in CC. This should probably be fixed before it is released on steam.