I think Freya, Amarant and Quina aren't relevant that much. But in a couple ATEs, Freya gets Amarant to talk about his past a bit, which was pretty cool I guess. IX definately makes the least effort to incorporate all the main characters in the story, but then again, it's hard to when it's mostly about Zidane, Dagger (with Steiner tagging along as her protector) and Vivi. Eiko, as one of the last summoners, is pretty relevant for most of the game.