^But that's rather the point. The game (or rather Kreia) asks is black-and-white morality a tenable world view? Can any decision be that simple? They even exemplify this almost as soon as you land on Nar Shaddaa: after seeing you help out some homeless guy, a beggar approaches you and asks for a meagre hand out. If you refuse him, he may go hungry, but if you do the compassionate thing, some other street dweller sees what you give him and as soon as he rounds the corner the bloke you helped is soon beaten up and mugged.
It also looks at the role of Jedi and Sith. Where the Sith are perpetually locked in a cycle of betrayal and self destruction, the Jedi are committed to coddling weakness, in those they profane to protect and even in themselves by relying so totally on the force.
I agree that KOTOR 2 examining the middle ground of the Star Wars Light side/Dark side conflict was an intriguing plot and refreshing as well. I actually like this plot better than KOTOR's due to its ambiguous nature. Kreia is a great foil in my opinion. She challenges both your light and dark moral decisions.
Although it technically isn't canon I think KOTOR 2, as well as KOTOR to an extent, are a good explanation as to why the Jedi are seemingly so stupid in the prequels. They have a narrow view of the Force and morality, which even Palpatine hints at. Of course Palpatine then goes on to prove Kreia's point by losing everything he's built by being overly arrogant.