First one by a mile. Better story, better characters, better settings, and the most amazing plot twist ever in video games. Except for maybe something in Bioshock
I don't remember the second one very well but I remember not really caring about the characters and all the settings being dead and depressing. Also the thing that REALLY pissed me off was the way they wrote off Revan off-screen, promising some huge future story that never materialized.