Bastila is deep because she reflects the whole theme of the game's Light vs Dark story, which I believe was:
Both the light and dark have their extremes, but the truth is somewhere in the middle.
Yes, she blindly tells you to follow the councel's philosophy over and over again, but all she is doing is repeating what she has been told all her life. When you dig deeper into her character you find that she has trouble accepting those rules hereslf. When Bastila fell, it wasn't because she was tortured, but it was her own resentment of the Jedi's laws that did her in.
Just bacause your interaction with her was brief, it does not by any means make her shallow.
As for Jolee, I take that back, he wasn't filler material, but provided more insight into the game's theme.