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..
You misunderstand my point, and clearly you misunderstand the game. I wonder if it's really worth explaining it to you...
As Anakin memorably pointed out in Revenge of the Sith - Evil is not an objective term, it's a point of view. What the Jedi and Republic consider sadism, the Sith and Imperials consider ruthness. And the Jedi's restraint on emotion is seen to the Sith as mental imprisonment, and to the Empire as sanctimonious. TOR makes clear that the Republic are enemies, and to the people of the Empire they are to be feared.
In NO Imperial class story or world arc is the 'Empire' the "villain of the story", Darth Thanaton was archaic, and Darth Baras was a usurper - both the Inquisitor and Warrior are clear that defeating them are in their, and the Empire's best interests. As does the Agent, regardless of his/her alignment.
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.
Nope, it's clear to any player that neither the Empire nor the Republic are going to lose. For that is no place for a story driven game that accommodates players of both factions to go. When the final ever piece of content is added to TOR, it will not feature the end of the Empire. Of that I am certain.
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.
Saying it comes down to "game needing to accommodate the players" is meaningless, as it totally ignores what my original point actually was.