I think you hit it right on the head. The problem with the way DS and LS are portrayed is that they are incredibly unrealistic. Let me illustrate by applying this to how KOTR2 would treat a real world scenario:
You're walking along and a homeless guy approaches you for money.
LS: You give the man most the money you have because you actually don't need the money (after all, money is pretty useless in the game)
Neutral: You ignore the guy
DS: You shoot the bum because you can, then laugh maniacally while twiddling your mustache.
With a more realistic interpretation of LS/DS:
LS: You give the man most the money you have. This will set you back considerably and make the game much more difficult to complete.
Neutral: You give the guy some pocketchange - enough to get him off your back but not enough to inconvenience you.
DS: You keep the money for yourself because you need it more than the homeless guy. Maybe you throw in "I work for my money, you work for yours. Get a job!"
I'd like to see a game where being LS and helping other people will actually cost you something and might even hold you back or weaken you. You buy a ticket for a woman trying to flee the planet. Well, now you're down 500 credits, you can't off the planet yourself, and the only way you can earn that much money back in a LS manner is by pushing crates around at the dock.
Perhaps this woman turns out to be an enemy. She later comes back and seriously hampers your efforts (like kills one of your companions or steals all your items). Perhaps helping this woman gets the local authorities after you. Not in the sense of KOTR2 where you can mow through everyone, but in the sense that if you're caught in the open they can and will kill you. Now you're stuck sneaking around town and hiding from the guards. But perhaps since you helped her, she will help you out later in the game - but if you are true LS, this shouldn't matter at all.
I'd like to see a game where being DS has tangible benefits, such as giving superior special abilities or items. However, if you're too DS and selfish, you will make more enemies that will cause trouble for you later.
Basically, I would like to see a game that treats DS/LS in a realistic fashion instead of the Saturday-morning cartoon manner it's treated now. Sorry about the long post/rant.
-Someone looking for a more mature game