Interesting points being made here.
1) Disciple as Historian: I think it would have been fun to hear some examples in Jedi and Republic history, especially as events cropped up where he could draw parallels. It also may have been amusing to poke holes in his theories on how he thought things happened and how they actually occured. As Scorchy pointed out in his walkthrough how he misinterprets Revan's history for example: A Jedi Fan Boy flunks a history test
2) Spies and Dark Sides: I think his work as a Republic spy should have been discovered by the Exile (after Kreia and Atton preferably) if you asked the right questions, had a certain amount of influence, and had a significant amount of points in Awareness. Having exposed him as a spy, then an Exile could either "keep him pure" or corrupt him - explaining how his undercover abilities have been easted working for the Republic.
JediExile, I think that the Exile was slated to train Disciple but he never got to receive his training because she followed Revan to war. As many of the other Jedi also went off to war, there weren't enough teachers to give the training. Yep, Dusciple got the shaft. (It would be interesting if he was a bit more angry about that - more dark side stuff to exploit.)