It's not the Nero brothers.
The riddle:
My calling now is not too far from what it was before
though I don't play with you much, friends and peers, not anymore
I am tired, weary; Do I even still exist?
I can't feel my limbs, but through my work I will persist!
Though short, unknown and ugly may all well be in command
they do not see how they are mere puppets under my hand
Incorrect answers:
Black Mages
Kuja
Vivi
Genomes
Garland
Necron
Cid
The game
Steiner
Lav Layderce
Queen Brahne
Queen Stella
The pointer
Master Phantom
The player
Black Waltz #3
The Nero brothers
Hints:
The answer is not anything inanimate.
The answer exists in the game's world, i.e. it's not something the player could be aware of but not the characters.
"Short, unknown and ugly" are epithets of three characters, although not any of the main characters.
The riddle contains references to a previous Final Fantasy.