I think the main problem with it was that there wasn't a clear story to it. In Jedi Outcast each mission continued the story, whereas in Jedi Academy it was just a mishmash of 'stuff'. It's a shame really, there are alot of elements to Jedi Academy's story that would've made it a great game.
Oh and Rosh Penin was annoying as hell, he's like the jar jar binks of the OT EU universe