I got that game with the Swords and the Mananserfants

[A Black Falcon]

First, SD3 is set before SD2/Secret of Mana. Like, hundreds of years before, I think...

Second, it's got lots of variety. There are six characters to choose from, and you choose one as your main character and two as the other members of your party. Each of the six characters has a somewhat different quest with a completely different beginning section and story differences throughout, and some different bosses at the end... but the story doesn't suffer for anyone at all by having more stories. Having just one would have been fine, I am sure... but they put more in. Of course the customizability stuff went farther in Legend of Mana, but SD3 was really the start of that and it's great in it. Oh, SD3 is pretty linear once you choose your party, but there is still replay value even within parties because at several points you can change your character into better forms on a branching tree...