Well the thing is, at the end of the day a good portrayal of good and evil choices is often one of subtlety. And let's be honest with ourselves, subtlety is something that this medium doesn't tend to excel at, and as a consequence, evil actions have a tendency to end up...well, cartoonish. Let me give you a little scenario.
Choice: Do you put money towards funding this orphanage? Y/N?
Consequences: For funding this orphanage you get Light Side points. For refusing to fund this orphanage, you get Dark Side points...and 50 credits from Snidely Whiplash.
Criticism: Now the above seems like a pretty reasonable distinction, doesn't it? Well, the light side option at least does. The Dark Side one...kinda stupid all things considered. That aside though, at least the Light Side reward seems appropriate, right? Wrong. The action itself appears altruistic at a glance, but motivation can change that interpretation dramatically. If you're doing it because you honestly sympathize with the poor kids, then yes, Light Side points would seem appropriate. But let's also think about this from a smart villain perspective for a minute. Funding an orphanage provides good press, which is useful to a Lex Luthor like villain. A Sith might check in on it every now and again to find a youth strong enough in the force to warrant training as an apprentice or an assassin. A warmonger might construct it near a military zone to deter enemies from bombing the area. A mad scientist might see it as a source of test subjects...in truth it's remarkably easy to justify an evil character not only doing this 'good' choice, but making use of that fact, especially if we use the same low standards seen in the original results.
Here's another fun scenario. You're the Dark Lord of the Sith, waging war on the galaxy, and doing a remarkable job of winning that war. You're in the middle of conquering a system, and you're faced with a choice. You can either decimate the planet, or preserve as much of it as possible. Which option's the Dark Side option? Trick question. First option's arguably more evil, but in it's "Stupid Evil". The latter option preserves more of the planet's infrastructure, ensuring they remain useful to you and that you don't end up emperor of a thousand and one garbage planets. What's more, you can use that to help fuel your war effort. With that motive in mind, BOTH can be considered Dark Side options. And yes, I did borrow that example from the backstory in KoTOR.
That is where morality systems seem to always fall apart, from what I've seen, they tend not only to sell evil actions short, but also tend to judge the action more often than they judge the motive, which strikes me as very shortsighted.