One complaint I've always had about this otherwise awesome game is that some of the characters get overshadowed by the rest of the cast as the game progresses. It seems like for most of the game the story is all about Zidane, Garnet, Vivi, and Steiner, and characters like Freya, Quina, and Amarant are only relevant when you first get them. Especially Freya and Amarant.
Even in a game with a huge cast like FFVI I felt that the characters all got fair treatment. This was probably because each one had at least one side quest that helped them develop. Yet I don't remember any end game quests that center around Freya and Amarant. Quina at least had the frog quest. Maybe there were some others and I forgot them. It has been a while.
It's a shame, because I really would have liked to get to know some of the less relevant characters more.