I don't think this is a choice with pros and cons, unless this game has any severe class balance issues, which there is always some, but i doubt it will be anything major in a Bioware game.
It's like Typho just said, it really depends on your personality and what you prefer in your own Star Wars fantasy.
If you like credits, treachery, doing your job your own way, and hunting down important individuals vital to the war effort, go bounty hunter!
If you like loyalty, teamwork, uniformed discipline, going by the book, and watching legions Sith explode in general, go Trooper!
Either way, take the best bounty hunters and troopers and pit them one on one, it's going to be an epic battle to please even the most testoterone pumped boys out there.