Have you not been having conversations with your companions? Or are you just not paying attention?
I must admit, that for both SW and Scoundrel I basically only played with two of each class's companions, which means I only gained affection with them, and therefore only had conversations with them - again, except for the few times where the whole crew gathers around the holo-thing.
But I find it weird that in spite of the fact that I almost only played with Jaesa once I got her, and tried my best to gain affection from her by chosing the right dialogue options, I still hadn't enough affection to finish her story, when I reached lvl 50.
Affection and companion story progression is too dependent on companion gifts at the moment, I think. I mean, if you can barely finish the story of one companion though you use that companion during most of the leveling, it's impossible to ever finish all of them unless you buy a ton of companion gifts. Which is artificial.
I wonder if it's because my reference point when it comes to companion characters is Baldur's Gate II; in that game, because all companions are with you all the time, your relationship with them as well as their story progress much more organically and quite often as well.
I think also Kotor I and II worked better than SWTOR in terms of companions; instead of affection, it was simply time spent with the companion that unlocked the next stage in their storyline.
I didn't care at all about e.g. Quinn. But had I known that bringing him for half the quests on a planet would have triggered a stage in his story for sure, then at least I would have had an incentive to give him a chance.
Companion characters is a really good idea for an MMO. But something is lacking at the moment, I think.
Happy to hear that most of you seem to feel you have had a satisfied experience with companions so far.