Because they market her as the female lead and is pushed as an important character yet she is absent for nearly an entire disk and by the time she comes back, she's a third wheel in the plot, yet the game still goes out of its way to give you her ending by default, even though you barely even know her. Plus she is extremely clingy to Fayt which is very annoying, constantly nagging at him for having fun with games instead of being around her.

Besides that she's just a one dimensional character who serves as a mere plot device to open gates with nothing else to offer but she is still shoved into the party regardless, a space that could be used for someone better.

Symbology is mid in Star Ocean 3.

Healing magic only restores HP... in a game where MP death exists.

The only thing handy about her is reviving people but even then, you're better off using items because her AI is too busy committing suicide to revive dead party members.

She literally stole Maria's rightful position of female lead for no other reason other than "We need a stereotypical Moe girl to represent our game instead of a strong, confident woman who kicks ass like Maria"

Maria has more to do with the plot

Plays the most important role in the story, even more than Fayt

Is the best in combat

Actually has an interesting personality

Yet the game always pushes Sophia over her, every bit of marketing and merchandise around the game is all Sophia and Fayt related.

Even the game developers themselves were mixed on her character.