Like seriously, every Imperial Character that I learned about in the comics and the novels died. Malgus, Baras, Angral, and Thanaton played important roles in various media just to die in somebody's class story, or for Malgus, a flashpoint. Then they also killed Kilran and replaced him with somebody incredibly boring. Also, approximately half of the Dark Council dies. The Emperor also gets his arse handed to him. What is with this? All we are left with is Darth Marr (the boy who lived) and the rather dull Grand Moff Ilyan Regus. Why can't the Empire have some interesting characters, besides the player characters themselves? It just makes the Empire a much less interesting faction.
I've always seen Baras and Thanaton as being representative of elements of the Empire that needed to be removed were it to have a chance of winning.