Knights of the Old Republic, the original, gave the player a very difficult choice at the turning point of the plot (the revelation of their previous identity). It gave you a better reason to possibly turn on the Jedi, I think, than its sequel did. Yet the path of the dark side is more interesting in the sequel, I must say, and I think Kreia is the key to that. She also makes life on the light side more interesting, though, so I should not say much. (I am a Kreia fanatic. I love that her very first line made me feel guilty. 'Find what you are looking for among the dead?' I knew from that moment I would love her as a character.)
My true misgiving about Knights of the Old Republic II is the heap of bugs I encountered. Far more than its predecessor.
Oh, that, and Sion. I did not find him a compelling character. I never did find corpse-villains the most interesting, and the 'Zombie Sith Lord' theme did not work for me.
But he was far more interesting than Malak, in my opinion, so perhaps I am not being fair. I simply found the wisdom of Traya/Kreia and the nature of Nihilus' power to be considerably more... poignant, or something to that effect.