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Bow from Breath of Fire II. In a normal situation he would be an interesting character, but he leaves the party so early and joins back so late that by the time you can use him again he's lagging so much behind the rest of the team that he is useless.
Bow had the best healing in the game, a bow that could shoot twice, and a great fusion if you wanted Rin in your party(you wanted rin in your party). By no means was he useless, and he was easy to catch up to your party in any case. It's a trap to believe he was useless just because he came back into your party so late.
Peco from Breath of Fire III
He isn't bad once you level him, but you have to actually make an effort because he starts at level 1 when you obtain him.
Him starting at level 1 was the point. The master system of the game meant that you had to watch your leveling carefully depending on what master you set to each character, since they influenced your level up stats. Peco becomes the strongest character in the game because he'd have no wasted levels without a master, and if you do it right, no master overleveling.
Lymle from Star Ocean: The Last Hope. Aside from her awful, awful dialogue, she's the slowest character on the battlefield. Her physical attacks are slow and weak, her attack magic is very quickly outclassed by Myuria, and her healing magic is outclassed by Sarah. Even Edge can use basic healing techs, so she's pretty useless once the party expands.
Her physical attacks are slow and weak because she's a mage, you don't do those with her. Everyone's healing magic is outclassed by Sarah. Lymle's got one of the best dodges (and back dashes) in the game, outclassed by only Meracle and Bacchus. This also makes her decent at medium range as she has more than just regular spells, she also has her Cerberus attacks, a lot of which are greatly disruptive in regular fights. If you wanted Star Ocean 4 useless, Faize was already mentioned, and Edge is pretty down there, but not totally awful.
I don't remember if he's useless or not, but I remember be a little pissed when this guy joined my group in Star Ocean:
He's not useless, but yeah he came out of nowhere and it was pretty annoying if you didn't know about it. He's a mage, a healer, and has access to earth magic which could be useful, i guess.