After playing both games recently, I've been thinking about which game I like more. So I decided to make a brief comparison of the two.
The first game strikes me as being much more simplified than its successor, both in gameplay and story. I like the simplicity of the story of the first game while at the same time, can admire KOTOR II's story, which is much bolder and experimental than the first.
For example, the story of KOTOR centers around two pretty straight-forward choices: either saving the galaxy from the evil Sith empire and Malak, or taking the route of taking it all for yourself as Darth Revan.
KOTOR II is a much different game. It's definately darker, gloomier and more philosophical than the first game, centering around spiritual concepts of the Jedi and Sith and the meanings these labels hold, as well as the concept of being a Sith at your core even when identifying as Jedi, as exampled by the fall of Atris.
The dangers of blind adherence to the religious codes and doctrines of the both the Jedi and Sith are outlined and the lines between what's truly good and evil are quite masterfully blurred by Kreia/Darth Traya, which really makes her a great antogonist. She's like a demon in disguise that whispers half-truths in your ear to try to influence you into the dark side, and she's quite good at it.
The concept of fear was also central to the remaining Jedi Masters who, wrongfully, assumed that the Exile had the power to cause the end of the force and therefore used this as justification for trying to cut the Exile off from the force. In this, even a Sith such as Kreia became somewhat of a savior to the Exile in showing that the exact opposite was true. This showed some pretty decent writing on the part of the developers.
As far as gameplay goes, there's much more of an opportunity in the second game for customization, which is fun but with the drawback of becoming massively overpowered fairly early in the game. The first game also has a level cap of 20 which moves and coincides well with the flow of the story, which I think works better.
As far as characters go, these are my ratings based on how interesting or memorable they are.
KOTOR
Carth - 7/10
Bastila - 7/10
HK-47 - 8/10
Jolee - 8/10
Canderous - 6.5/10
T3M4 - 6/10
Juhanni - 5/10
Mission - 4.5/10
Zalbaar - 4/10
Darth Revan - 8/10
Darth Malak - 7/10
KOTOR II
Kreia - 10/10
Atton - 7/10
Atris - 8/10
Bao-dur - 5/10
Handmaiden - 5/10
Darth Nihilus - 4/10
Darth Sion - 5.5/10
G0T0 - 5/10
Hanharr - 5/10
Mira - 4/10
Disciple - 3.5/10
Visas - 7/10
The Exile - 6/10