I would much rather have a list of characteristics that you could choose from as a player than authors could then pick-up on in their missions.
Take a look at this old thread by Leviathin99, http://forums.startrekonline.com/sho...d.php?t=157357
The idea of having a character profile panel for your captain and BOFFS that let you select a number of personality traits, likes/dislikes, friends/enemies, is exactly the type of thing you are looking for to personalize your missions.
The question then becomes, "what if the value is null/not-set by the player" and at that point you could go back tot he "note/warning" that this mission uses those values and you strongly suggest the player select them before playing the mission. (and use a default value if they refuse).