I think for the story in SWTOR, only the class stories of the Jedi Knight, the Consular, the Sith Warrior, the Sith Sorcerer and the Imperial Agent tie up rather well with the main story, despite it being repetitive with slight differences in dialogues, and the expansions. The smuggler, not so much. Republic trooper and bounty hunter stories I have not done but I've a feeling the last three won't actually play / tie in with the tapestry that well because they don't even move in the power circles that's populated by force users; Jedi and Sith. At best, they're a shoo-in just so they can take part.
The main story now involves the Sith Emperor very heavily. With Knights of the Fallen Empire expansion, they might play better but I still feel they're out of place. They should have an entirely different arena, secondary supportive roles, instead of being 'forced' to take part in the same scenario that's actually meant / more suitable / crafted for force users. I guess that's why I'm not very keen to update the smuggler, trooper and BH. They don't fit.
The Imperial Agent is entirely unique, I won't post spoilers but her influence is far greater than the smuggler, trooper and bounty hunter. However, it's still rather weird to have her facing formidable force users and walk away victorious.
*shrug* Ok, maybe she has a bit of the force. 
Darth Marr is a rather interesting Sith power figure. He is ambitious but he's also pragmatic and willing to listen. However, it will take more in the expansion to know him truly.
Suresh is the republic supreme chancellor (ultra moron). 'nuff said. I won't be surprised if Grand Master Satele Shan filed late reports and never tried to bring up the matter of the Sith Emperor on Yavin 4 with her until it's all over. Her statement "Don't tell me how to fight a war" makes me want to kick her out of her comfy chair. She's a desk flying senator for crying out loud. Idiot twi'lek. I hoped she gets it after what happened on Ziost (the final conclusion to chapter 5)
Grand Master Satele Shan, I've no idea if she will appear in the expansion but I hope she survives. More Jennifer Hale! 
Lana Beniko and Theron Shan. New chars for the C5 expansion. Also new LIs. Tried both. For a Sith, Lana is surprisingly open, regarding the relationship. Of course she could be just playing a game (Mata Hari whatever) but she floored me with the last thing she said, which is more than what Theron said. He talked about the intelligence service he's going to back to, she talks about parting, the necessity of it, to be focused on her job, the troubled future and finally, a warm farewell. Theron... you suck. I don't even remember any sweet things you said, if there were any.
Lana is better than you. 
I am looking forward to KotFE since these two will be the new companions. 