While the idea of species-ism may not make sense to most, it is there, and as others have pointed out, it goes Sith -> human -> all other aliens. I'm going to wrap the below in spoiler tags, simply because it involves my experience playing a Chiss operative. Actually, maybe its not really species-ism, but elitism. You have the ruling class (Sith), the military (Imperials), and then everyone else.

As others have posted, my hope as well is that they continue these class storylines in the expansions, since they've done a marvelous job with them so far. That being said, I can see them creating a single connecting storyline for the expansion as well. They could create brief "detour" quest lines, that focus on at least 2 classes, so that while every class would experience the main missions, you would experience the "detour" only twice for each faction. For example, on the Republic side, every class completes Quests/Missions #1-5. At this point, a "detour" occurs, so that Jedi Knights and Troopers experience #6a-10a, Smugglers and Consulars experience #6b-10b. The mission line converges again, and we move on. Its an idea anyway, and I know that alot of work would still need to go into it to make it happen.

I'm happy that its not a full-featured space flight simulator, because it gives everyone the opportunity to participate in it. Does it appeal to everyone? No. I am grateful though, I don't have to plug in my joystick and throttle to enjoy it. I personally, am hoping this update that was mentioned, involves multiplayer PvE space combat. For example, a flashpoint style mission, where you are shuttled out to a battle cruiser, and then dropped into a fighter, and sent to destroy some enemies, or satellites, or whatever, and then have the same decision mechanics involved.