A great idea inspired by athropy's questions, the Freespace command line is not like those found in FPSes. Instead, the command line is meant as part of the game-and if a better alternative can be found, it should be used.
The base idea is implementing dynamically changing SEXPs in-game, as defined by the mission maker. The basic format would be
if player_command_equals 'lay in a course to %1,%2,%3'
So, if the player types in 'lay in a course to 1,2,3' at the FS command prompt, a waypoint would be set at coordinates 1,2,3.
A very simple logic statement, yet worlds more powerful than what we have access to now. It would only require one more SEXP, I think, the "player_command_equals" SEXP. This SEXP would look for that occurence of the string, and set the "%*" variables for use in the results of the function, like the above example. %1 is where the player puts the X coordinate, %2 the Y, and %3 the Z coordinate. The values inserted there will change the location of the waypoint.
Or it could be something like
if player_command_equals 'reverse the polarity of the deflector array'