So I have been reading a lot of dissatisfaction with the current affection system.
The frustration seems to lye with how certain companions react to your choices. Some have even avoided side quests, trying to navigate this invisible logic.
Suggestion: have a morality meter tied into the character's choices (kinda like KOTOR), and a favor system that is based more off personal interaction such as: "MY STARS!, you SAVED me!" (Corn fully intended).
If there are "personal bonding" checks made, than the companion could begin questioning their own moral choices and how they view the world. (become less selfish, for example).
The beauty is that such changes don't occur overnight, and can be written into future chapters (its the end of the story that matters most).
Replay-ability: You can see different aspects of the same person and how your choices mattered.
The other real concern for many is having companions that people actually look forward to adventuring with.
Footnote: If you have read any of my posts, my current companion choice is "non of the above". I am trying to make positive suggestions, as I have heard many of my concerns echoed load and clear.
I have a post in general asking what would be your ideal companion, and I have hoped (but am not set on) finding one companion in my party that I could bond a little with for immersion.
The above suggestion is a very rough concept, but could go along way to making the Dialogue system (that you have invested so much time in) pan out.