The system worked well for KotOR, and it would in SWTOR if not for having some gear unlocked by your level of ligh or darkside. (that still annoys me a little, I may roleplay as much as I want but at the end I'll just end up farming the first flashpoint for ligh or dark V to get better gear)
The choices weren't outlined as to which are good and which are bad, but they were easy to guess which would give you points for each side. It works well with star wars and jedi/sith because light and darkside are a sort of inuniverse reality (in the lore it has also been discussed that they don't exist, that the force just amplifies everything in a force user, meaning that instead of being menacing one just slams a person into a wall if he doesn't have selfcontrol)
But for ME, what is supposed to be a more morally complex story it doesn't make sense. Specially since it falls back to that swtor, instead of better gear if you want better outcomes choose red or blue path.
And it's been talked about but I support not every seemingly good choice leading to good outcomes. For example, in Deus Ex: Human Revolution you get at one point a secondary quest. There's a very small glitch (like getting a bit of lag in the HUD, it's ingame, happens very rarely) in the implants and they announce that they've found the solution. So the quest is to go and have them fixed, nothing to pay, just get into a clinic, say you're there for that, cutscene, experience and money. There were sme people cynical about it, and you investigating some people with ties to them could make you cynical about it too. And easy quest that shows the clinics doing a real job, more inmersion, that's good.
Now when you face one of the bosses it is revealed that it was all a trap, part of hte master plan to create mindless pawns out of people. If you had the implants "fixed" you lost your HUD and you implants, having to rely solely on weapons (no cross to aim either) for that fight until you found a scientist that fixed it, it was part of the main campaign so you couldn't miss it.
And this was great. You had the choice of fixing them of not, which was a simeple sidequest turned into something important with consecuences. Fixing them was technically the good choice to do. There's a problem, why not fix it? And it had a bad outcome, and that was fine. Yes, you can argue that not fixing them is the good choice, but the first time you do it you have no real reason to say no to them, the only people saying no are kind of these paranoid cynics.
And I think that is what we want. Choices with consecuences in which the first time at least, we don't know which is the good or bad option, and that if you roleplay, none of the two are better than the other or at least not that much better. And this one didn't have a neutral option, you either went into the clinic and do it or not.