Well, FFIV is considerably older than CT, so that might have something to do with it...CT's graphics haven't dated quite as badly. Also the Chrono audience is considerably smaller than the FF audience, given that there's only been two Chrono games and it seems like most people who played Chrono Cross (except for me) weren't a huge fan of it, whereas zillions of folks have played the FF games and so there's a larger audience.

(Or, more cynically, they have to do a full remake of the FF games because they've already rereleased them twice over with minimal extras, on PSX and GBA, and they figure they need something more to get folks to triple-dip; whereas CT was only rereleased once, on PSX, so they can get away with releasing an enhanced port once more before they have to fully remake it on the third try, as with the FF games.)