Hard to choose just one. The series as a whole suffers from main party characters with limited story arcs. FF9 often feels like the writers were like "ah trout, we haven't done anything with Amarant, better give him some story here, and then forget about them for the rest of the game". They try to hide him behind some enigmatic characterization, but they fail, because as soon as you get a look behind the curtain he is quite uninteresting (I think they improved on this model with Kimarhi in X).

Freya is a prime example of someone who is interesting and welcome at the beginning of the game, and then becomes just-another-party-member for the rest of the game. A short story arc, then zip.

There are numerous examples of this: as a rule, main party characters are dealt with sequentially, and then ignored. No two characters are allowed to develop at the same time, they each get some spotlight and then are kicked off stage.

I would also change Vaan. He is someone who is presumably the main protagonist (at least from the beginning), but who is at the same time absolutely uninteresting. He's more or less an avatar you move from place to place so other characters can develop.