i've never had that problem, since i don't use invert (in fact i need to be able to invert-invert in FS winknudge), but I agree that is a basic option that can't be difficult to do and should be included. my main gripe though is the PISS POOR response to mouse movement in several of the last few games i've played. most notably and the worst offender, crysis 2. aiming isn't smooth AT ALL. you have to move the mouse a fairly substantial distance to get that first bit of movement out of the crosshair (or throw accuracy to the wind and jerk), and when it finally does move, the granularity is several pixels at a time. i know it's not my mouse, because it works BEAUTIFULLY in crysis 1 and plenty of other games with the same mouse settings (which IIRC are full sensitivity and acceleration/smoothing enabled. it creates situations when i'm trying to snipe at significant distances where i literally can't line up the shot properly, because the crosshairs jump over where i need them to be. hell, even close range aiming is harder than it should be.
.... so yeah, joysticks are awesome for freespace.