Schala's got the hair, and she's got the name. Popularity was guaranteed.
I was going to suggest that Schala was poorly written, but stopped myself mid-type. Sometimes it's a character's flaws that make them stand out the most. It's Schala's personal tragedy and human failures that give her story oomph; I'm not sure there's a single Schala fan who actually looks up to her, or wants to be like her.
Now that I think of it, Kato probably designed Schala as a thematic foil to Crono & co. Also, with the turn in popular opinion regarding Magus' mission (I think the majority view is that he was out for pure revenge and didn't care to save Schala in the least during most of CT), Schala amplifies the pure horror of Magus' mission. Her weakness probably sickens him to the point that Magus' mind dehumanizes her, allowing him to use her as a simple stepping stone to further his goal.
The ending of Chrono Trigger suggests, and the CT:DS bonus ending solidifies, the fact that Magus had a change in heart somewhere along the way; probably when he reflected on Death Peak after Crono's friends save him, and he still had a total lack of motivation to rescue Schala in the same way until it was too late.
Masato Kato might be one of the great literary geniuses of our time.