I never had any problem when choosing LS/DS options in most of my toons, except for my inquisitor. And I'm not talking just about them being illogical, but also most of the times they're just...so stupid funny!
You see, I've read a lot about how evilly corny was a dark-side sith storyline. Then when I played a full dark-sided pure-blood juggernaut, I found it was very entertaining. Sure, there were a couple of funny lines but overall, I felt great to be a dark lord of the sith! I really enjoyed playing it.
But my inquisitor doesn't feel right at all: choosing dark options made me feel like a freaking psychopath ( -insert evil genius laugh here- ), and the light options most of the times doesn't make sense.
I don't know, but sometimes I feel the writers made the whole inquisitor storyline based on that popular character from the Stephen King's novel: "IT" the psycho killer clown.