To implement an all encompassing system whereby a mission designer could overwrite player preference with command lines on a per mission basis? Ie., implement a little command line editor in the mission specs editor where you could force command lines on or off?
I ask because a lot of the more recent command lines are less about the core ways the game runt (-htl, -jpgtga, -pcx32 etc.) and more about graphical stuff ( -nomotiondebris, -phreak, -newradar (or whatever the 3d radar one is). This is the sort of stuff that can be applicable to mission designers. For example, when you go on Vasudan Exchange, it might be nice to force the player to use the new radar, the new -phreak scanning type etc. to enhance the sense of difference and change. Also, a lot of this stuff is going to be applicable to atmospheric missions. We're going to have to fiddle with getting the lighting conditions right for one thing, which is probably going to involve a high ambience setting.
Obviously there are going to be some problems. For example, I expect trying to turn on HTL mode halfway through a campaign would not be recieved well by the engine. You'd also have probalems with different builds not accepting different command lines. With suitable warnings however (both to the FREDder and the player (This mission requires at least FSO version 3.6.whatever)), and a certain degree of trust in the FREDder not to ignore those warnings, I doubt there'd be too many problems springing from that aspect of it. After all, worst case scenario, it's a bug in the mission and nobody plays it. That said, I don't really know if this sort of thing can be coded at all, let alone how difficult it would be.
So, err, any chance?