One of the biggest cons of supcom in terms of moddability was the inability to use the io module and load external libraries.
It'd be great if the loading of "dangerous" libraries could be switched on with a command line argument. (as far as I know it's pretty simple to enable / disable builtins of lua in c...)
That way GPG could make the user take all responsibility when manually creating a shortcut and enabling the command line... (or so I hope, I'm not sure how this goes legally)
You could even warn the user that the loading of "dangerous" modules is enabled in the game, and tell them which mods use them.
Call it /dontenablethis or /dontblameus or even /thisisavirus so users don't enable it blindly, but whatever 
It would make things so much easier.