Technically, if you try to look on story with distance, it isnt so bad. You seeking knowledge, cure people, then you became something like jedi lord (really, this title actually existed in some age), who creating own forces by helping allies, make own "army of light".
But companions and even JC story npc pushing every good ideas back. It looks like writers was tired from other storylines. Only good companions are IMO Zenith and Holiday, of course
Nadia is like spoiled 13-year old girl, but not so much worse than Ashara. Rest of them are just boring, and that lizard guy is probably worst - creepy, annoying, boring...perhaps only Skadge is worse than him.
Another big problem are little 'details' in storylines, what makes players tired or frustrated. Just start with 1. chapter: its basically just - seek crazy jedi + use power on him/her. thats all. Jedi Knight had at least some fresh sidelines of story, what helped your focus, like truth about Kira in the middle of first part.