The first time she appeared, it looked like she is one of the evil ones. As if her role was written to be evil and just rewritten as one main character missing for the good side.
Ironically it's actually Crow, her partner in the Arc Cradle duel against Sherry, who WAS a bad guy rewritten into a good guy.
Crow was initially going to become a Dark Signer, but Blackwings' popularity made the higher-ups force NAS to make Crow a Signer and the cost of downgrading Rua/Leo for almost 100 episodes.
Marta, the owner of the orphanage, is actually going to be a dark signer. She actually has a secret affair with Yusei's dad. But it turned out elderly characters have less appeal to viewers that's why they change the script and killed her early on the episode where Yusei and Kalin fought, when she was meant to be revived.