For CT, I like Janus the best, since he's so tied to the story and has a much more defined and complicated pathos than the other characters, who are just sort of the do-gooder type (which is enjoyable, but not as enticing).
I think my favorite character in the whole series, however, is Kid/Schala; like Magus, she has such an interesting back story and a well-defined and (to some extent) complex pathos. She is part of, IMO, the most interesting and engrossing relationship in the whole series which is that between her and Serge. Furthermore, her merging with the Time-Devourer makes for one of the most interesting last bosses in all of RPG-dom--all at once you want to destroy the Time Devourer, yet Schala's young and innocent face and her connection to Serge gives you pause. Great stuff.
