I have a similar dilemma. I can say that the Jedi Knight story is excellent imo, if you want a fairly straightforward epic "saving the galaxy" experience. If you try it, at least play until the second planet (Coruscant) as it was one of the best whereas the starter planet was among the weakest.
My son really liked the Bounty Hunter mechanics (as well as story) though, so I may go for a trooper next. I also like the trooper premise, although the JK was much more military-oriented than I expected. One thing I missed from the JK story is when the war breaks out - apparently, the trooper story is the clearest in showing that transition.
My limited taste of the Sith Warrior was very tantalising though - playing a light side role in such a dark setting was delicious and felt wonderfully subversive, but I don't know how far I could get without feeling morally compromised (I am not a fan of playing evil characters in RPGs).
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