I had to go with the Second Fire Bringer. S1 hooked me into the series long ago. The tragedy of the deaths of Odessa, Gremio, Teo and Ted was just so much more real than anything in any other game I played. (incidentally, what characters do [story] has way more to do with how real a game is than what they look like [graphics]. cough*Final Fantasy*cough). S2 also had an amazing story with even better gameplay elements.
But S3 had Luc and the Destroyers. Maybe the coolest name for a group of characters. As tragic as Gremio, Luc was way beyond. In fact, Luc is the reason this game is my favorite over the others. I don't like the battle system; I don't like the war system; I don't like Hugo as a main character; I don't like Chris all that much; (I like Geddoe, but I like him best with his Lightning, so he can't be the main character). Luc makes up for all of the other deficiencies in the game. His despair, depression, anger, cynicism, and malevolence make him the most real thing from all of the games. And I love that he dies. Quality characters die. Hamlet, Romeo & Juliet, MacBeth, Julius Caesar all died in Shakespeare's tragedies.