The ability to make choices, specifically choices that are associated with a moral alignment, is something new for an MMO, even if it was previously tried and tested in Bioware's single player games. Unsurprisingly, it's a feature that's encouraged a lot of discussion... however, I continue to be disappointed by how extremely superficial many of these discussions are.
"What the hell, Bioware? Everyone can obviously tell that you got the light and dark side options in this quest completely the wrong way round. How dare you give me dark side points for doing what is totally and obviously the right thing to do? My reputation as a good human being is forever tarnished just because you can't tell right from wrong. Seriously, your game sucks."
(As an aside, I don't think I've ever seen a dark side player complain about "unfairly" being given light side points for something they did.)
This is pretty much the general tone of many forum and blog posts that I've seen on the subject of light and dark side choices. Personally I feel that they are missing three important points.
First off, light and dark side points are not srz bsns. It's not going to be a black mark on your CV that you got 300 dark side points while levelling. In fact, did you know that once you hit Light V, all your previously acquired dark side points are erased? (I would assume that it's the same for Dark V and light side.) I was actually kind of disappointed by that because I felt that the dark side points that I had gathered while levelling up my otherwise very light side trooper were part of my character's history so to speak, and I didn't particularly appreciate having that history erased. That aside, you can still nudge your alignment back the other way at any time by doing repeatable quests, flashpoints or using the diplomacy crew skill, so getting a few points in the "wrong" column because you preferred the other story outcome certainly isn't a big deal in the long run.
Actually, your light/dark side points are something that has very little effect on gameplay anyway. I mean, they already took out the colour crystal restrictions based on alignment, and I wouldn't be surprised if they did the same for relics eventually. In fact, you could completely remove the entire light/dark side system and it would hardly change the game at all. You could still make all the same choices; the game just wouldn't keep a running tally of how many people you've rescued vs. how many you've killed. It's really not much more than a measuring stick that allows you to easily compare the totality of different characters' roleplaying experiences. Definitely not something over which anyone should fly into a rage.
Secondly, as far as comments about what's "obviously the right thing" go, I'd like to point out that even real life philosophers don't agree on how exactly to define good and evil. That doesn't mean that we can't have discussions about it, but it does mean that automatically dismissing a moral judgement because you know best and everyone else obviously couldn't do anything but agree is at best very narrow-minded.
And thirdly... it isn't even entirely about good and evil, it's about the Jedi code vs. the Sith code. Yes, the Jedi are the good guys and the Sith the bad guys, but it's not entirely black and white. "Being a good person is not enough to be a good Jedi." For example the Jedi disapprove of romantic relationships, which is why smooching people as a Jedi sometimes yields dark side points, even though few people would consider this an act of evil. So before you dismiss a dark side choice as incorrectly labelled because you don't consider it evil, ask yourself whether it isn't instead a question of what a Jedi considers appropriate.
Now, this... this is where I personally think things get interesting. Are the light and dark side gains consistent with the Jedi code? For reference, the Jedi code, as Satele Shan lectures you on it:
There is no emotion, there is peace.
There is no ignorance, there is knowledge.
There is no passion, there is serenity.
There is no chaos, there is harmony.
There is no death, there is the Force.
If you read the Wookieepedia page I linked above, it also has a lot of additional tidbits about what it means to be a Jedi, such as the whole thing about avoiding romantic attachments or defending the weak. To be fair, I do think that most of the decisions in the game align very well with this code. Calmly capture the bad guy or chop his head off in anger? I don't think I need to explain in detail why the former option does fit the light side and the latter is firmly dark side.
However, sometimes you come across a quest that makes you raise your eyebrows because something seems off - and that's something I absolutely agree on with the forum complainers! My personal favourite example of this is a quest from the Sith starting planet Korriban. You find the body of a failed aspirant and return it to his father, who is a temple guard. He's kind of down about the death of his son (unsurprisingly), but not exactly surprised. He then asks you where exactly you found the body, or in other words, how close his son did come to succeeding before ultimately failing. The truth is that the poor sod died almost as soon as he crossed the doorstep of the tomb you found him in. However, you are given the option to lie and make it sound as if he did a lot better than that.
Personally I thought that it was very obvious that the light side choice would be to tell the truth. Jedi aren't supposed to lie, and it's not like there were any excruciating circumstances at work here where lying would save someone's life or anything like that. So I chose to be truthful... and received dark side points. Huh?
On Republic side there is another good example of this on Ord Mantell. An elderly couple asks you to keep your eyes open for their missing son, though he is presumed dead. You find him alive, though he's been brainwashed and turned into a child soldier. You would think that the harmonic, truthful thing to do would be to send him home to his parents, who will be happy to see him alive and make it all better. Nope, you get dark side points for that, and he runs away anyway. I wouldn't swear by it now, but I might have received more dark side points for truthfully telling his parents about his fate as well instead of lying about it. What's going on here? Why is trying to help and being honest a dark side thing?
As I encountered more and more of these quests however, I began to spot a pattern, and one that can be summed up in a single word: compassion. Strangely, this is something that seems to be completely absent even from expanded descriptions of the Jedi code. Yes, Jedi are supposed to help the weak, but the main drive behind this appears to be a desire to "serve the greater good". There's nothing wrong with that in principle, but if there's no compassion involved, you can end up with people reciting "the greater good" in zombie-like voices while disposing of dissenters in most gruesome ways. No, Jedi can't be like that. Jedi have to be compassionate, even if they aren't supposed to be emotional. The game drives this home with lines such as: "Jedi save people, not buildings." It's okay to have some "quirky" rules in regards to relationships, but you can't be completely disinterested in other people's feelings if you want to be seen as the good guys.
However, this does conflict with the whole "being calm and placing the greater good above all else" thing... and suddenly I had my explanation for pretty much every confusing light/dark side choice ever.
Why is it a light side choice to lie to the guard about how his son died? Because it makes him feel better about his son's death, like the little fellow achieved at least something. The lie doesn't harm anyone because it doesn't make a difference to anything else. Personally, I still don't agree that this is more Jedi-like than being truthful, but I can at least see where they are coming from.
Letting the kid on Ord Mantell run away is light side because it means you respect his feelings about wanting to be left alone after all the horror he's had to endure, as opposed to trying to impose your (or his parents') will on him. Again, I still don't agree, because how much can you really trust the opinion of someone whose brain was completely addled only five minutes ago? He's hardly in a state to make well thought-out choices about his future at this point. However, I can see how it becomes more a matter of where you draw the line between doing someone a kindness and doing something that would lead to a bigger benefit in the long term, rather than simply seeing completely clear-cut opposing choices.
At the end of the day, we can discuss what would be the right thing to do all day, but Bioware had to pick one and stick with it. I absolutely do think that some of the choices they went for are debatable and even inconsistent in where they draw the line, but I still believe that its worth trying to understand why Bioware made these choices when they did. It might not officially be part of the Jedi code, but I do agree that light side characters are better off being portrayed as compassionate than not.