I spotted precisely one FFIX reference, and it was rather forcefully proven to be a pure coincidence arising from both characters being references to the same FFIII character. Did they really have to give him a tail, though...? Eh, I've said all this before and nobody wants to hear it. (Leaving this here, since it matters to discussion, but doesn't need to be dissected further, so please don't fight me on this.)

That aside, sure FFIX made pretty solid use of what came before, but I think it's more important that it was aware of everything that came after what came before. The aforementioned FFIII reference goes through the same basic destined amnesiac BS, only to instead tell the ancient civilization that birthed him to shove it; the badass female general isn't totally unmanned by love; and that oh-so-glorious reverse-Faris that Garnet pulls. There was even a moment during Ramuh's trial that acknowledged, and optionally apologized for, the rather unfortunate handling of character death in FFII.