Both characters are awesome i must say. ( Awesome as in...Awe inspiring, not Awesome as in "hehe, Sephiroth pwns he so awesome, teh n00b")
However, CT was the first RPG I played, I played it when I was 12, and honestly, at that age, your easily influenced, and this game got to me, and still does. The game was a incredible experience for me, and then I see Magus, some dark, villian like character, and then I later find out you can play as him. That, was just simply the best.
So for me, I guess it boils down to which character got to you/affected you most, and it would be Magus.
( Magus pwns anyway, so who cares about the rant )