I really liked how certain conversation or behaviour options turned you "heartless", "vindictive", or "altruistic".
What I disliked to no end, is the game immersion breaking need to save before conversations and then reloading if you got a trait bonus that you really didn't want, especially with 2 different characters - and on top of that then actually doing in game what you want to do in the first place while both characters get different bonuses.
(It only got better in late game, if you had enough points on a specific trait side, that one or two on the other side didn't matter anymore)
This could be solved by having the trait bonuses not be something like "Bartering +1", "Sneaking +1", "Immunity to fear", "Crafting+1"
Some of these bonuses save you 3-5 skill points. Or to good to true (I'm looking at you immunity to fear versus +1 on loremaster). Either the bonus or the saved skill points are absolutely *crazy* not to have, if you wanted to optimize your party. Or not waste skill points.
To keep this still very cool system of choices having an impact on the world / characters, you could implement :
-that certain NPC's react differently to certain traits, the tone of the conversation
-certain NPC's have different conversation options for different traits, improving replayability (if the different choices have different outcomes)
-follower's or henchmen could voice their opinion with certain traits displayed, good or bad (not that they'd leave you - if you optimized your party and they left you - that would be immersion breaking again, because you'd just load and choose differently)
-and countless other options that I can't think of right now ;) - but nothing that would require an optimized party to save and reload all the time
Just to reiterate, if I wanted to play a good-hearted rouge (in strategic mode for ex.) I would reload every time I lost the "+20% to hit bonus when backstabbing" bonus, and have to be heartless at least more that half the time because of it.
Since this is an RPG, having the role I want to play dictated by the bonus that I will get, is really immersion breaking (and kind of annoying - in a role-playing game).