The Empire loses more because the Empire is the bad guy. No matter how much BW tries to show that the Republic has all these flaws, in the end, everyone knows The Empire is the villain of the story. Whether the Empire is your favorite side to play on or not, it will always be the villain.
Storytelling doesn't mean both sides should lose equally either, just because there are Empire players. Empire is going to lose. You know that going in.
As for Bounty Hunters/Smugglers taking on Jedi/Sith. Why are you limiting it to those two? If you're going by the movies, how does ANYONE who isn't trained in the force able to beat a Jedi/Sith? Jango only held his own for so long and Boba we never really see fight Jedi. Boba at most ensnared Luke, who then broke out of it.
This basically comes down to the game needing to accomodate the players.