I think you missed the most important point of the game. (Okay, let's say the most important for ME.
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Spoilers ahead!
FFIX's story is not about fighting Kuja, it's more about fighting your fate. And fate is something you can't exclude from a description about FFIX.
So all the characters you said weren't important were important in that matter:
The Rat Lady, Freya. She had to find Fratley and she thought that she'd find him when she went with the others. So she had a good reason to join. Also, her home was destroyed by the enemy, so she WAS important to the story. She grew really important when she finally found Fratley - then all this stuff about fate began. It seemed to be a hopeless situation, as Fratley had lost his memory and nobody knew what to do. It was fate and she began fighting it. All the more reason to fight on.
Quina. I didn't really like him, but I didn't hate him, so most of the time I ignored him. Yet, he said some quite interesting things. (Quina is male for me ^^") Remember that he always talked about food? Yeah, that was quite annoying. Yet, did you see what he wanted to say? He often put really philosophical things into terms of food. I don't remember one of them, sorry, but I know that sometimes I thought that it was really intelligent what he said. It was of course also about fate and how to fight it.
The big red-headed dude, Amarant. He was important because Zidane ruined his life. At least I had the feeling he had. He was once an important person, a bodyguard if I remember correctly. And then Zidane came and ruined everything. Fate again. xP So he tried to find Zidane to fight him, but when Zidane didn't want to kill him after winning, he began thinking about Zidane and why he acted like he did. I found that quite important, as the player of the game surely also wanted to understand Zidane. Also, Amarant thought his fate was fighting Zidane - and either be killed by him or kill him.
The little girl summoner, Eiko. I agree that at the beginning she was more important, as only by meeting her you find out about Garnet's past. But she was also important in the end. Remember what she said about her grandfather? She promised him to stay in her village forever, but then she decided ON HER OWN to go with Zidane. She made that decision because she thought it would be better for her to see the world. So her reason for joining the group was.. some kind of curiosity. (Yeah, I know that she also wanted to be near Zidane, but such a little brat can't possibly know what "love" is, so this is no reason for me xD") I had the feeling that she also wanted to find out who she really was.
Another thing that made this game special and which includes all the characters: Life and Death. It's the reason why I loved the game: It's not only "rescue the world from Kuja", but also "find out who you are, why you live and why others die". I think Vivi showed that pretty good. All the black mages who died after a certain time showed that. They wanted to live so desperately that they joined Kuja and served him. I can't help myself but I thought about myself at this point - if I'd done the same. Then I fought about mankind generally - and saw that many people would've done the same. They do such things just to live on. The game perfectly shows how afraid we are of dying. I didn't see something that philosophical in ANY other FF.
In that point, I agree with you. There really were no hints, although I think that Zidane's Saiyajin-tail was a hint. I've always wondered why he had one and if that mattered to the story. But after meeting Freya I hadn't thought about that anymore. I thought that he was just like Freya - an animal-like human.
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