I don't think it would be too difficult to get a plot to exist in that type of structure.
Initially, the game would be exploring the Master/Apprentice aspect of the Force during your training, but your training doesn't even need to be that huge of a part of the game, and can be streamlined like metadigitial suggested.
The main plot would focus around which ever Master you have's desire to investigate Revan/the Exile. And you don't have to have grand scale differences between both ideas, as there'd likely be a lot of overlap of areas and whatnot between the two.
And thanks for the kind words metadigital.....
Seems as though Darque isn't interested in writing the middle though :D