why is the creature's appearance relevant? what "science" is shelley discrediting?

Shelley is discrediting the science of physiognomy

I assume that Shelley is challenging the “science” of Physiology, where the appearance of the body serves to reveal the personality.

Well first off, his appearance serves to propel the story. If the monster was handsome, he would probably be accepted, and there would be nothing else to say. Then, it could also be that Shelley made the creature hideous because he was created against divine laws. If the divine laws made creatures beautiful, then going against the divine would make them ugly. The appearance might also serve as a warning to humanity to not dabble in things that are legitimate territory of the divine.

His appearance is relevant to everything because no one seems to be able to see beyond what he looks like. The creature never had a chance.