All the stuff about the plague seems tangential in this game, and the only reason I can think of is that Trish isn't around? Maybe they should have started you off in Floodtown first? Additionally, the plot in general seems so much less elegant relative to the first, they telegraphed so many of the plot twists in this game from the start, not like with the first where you were legit WTF???? when you found out you were Kessler. Also, missing the comic book cut scenes this time, I think they did something for the game as well.