yes that is a problem. It could be that the plot 'forces' you to become either the apprentice of Sion, or a jedi master (my favorite: WHC) That would do away with the problem of inflated variables -but then, some gamers wouldn't like being compelled to join a Sith Lord, or Jedi Master, over and over on each replay. (Though no one got fed up last time, with the plot twisting over and over)
This assumes of course that we're 'becoming' the apprentice -based again on what the devs. said earlier, that the master-apprentice theme is somehow worked in this game; I can't imagine how 'having' one could work. You start a level 1 char. yourself. At what level do you take on the apprentice? To what level *can* you train him? How well can you attend to him, and what sort of a teacher-pupil relation can it be, while the game is heating up and you have little time to give lectures. Why would you want to have a level 6 character in your team when you're level 18, etc.
Now it could be the case that the game explores the master-apprentice relationship without us becoming masters or apprentices: It could involve the rescue of a master; the redemption of the master or apprentice; the elimination of a master (DS), etc. Countless variations can be thought, over these motives, and in connection to the characters.
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Simple, you just can start to train someone as your apprentice when your alignment is fully light/dark, thus fully understandment of the force