First off, the idea of the Gems being magical bothered me from the beginning. I could deal with it but it seemed random and unnecessary. Energy beings who's physical forms are tied to their gems I could understand. But magic? I never saw anything that really looked like magic. Just sparkly science stuff from an advance alien race. Peridot didn't strike me as magical either. Then I realized, maybe the Gems aren't really magical!
Let's review, they've been on Earth for thousands of years. Pearl even remembered when humans were a hunter gather society. Remember back in the day when people believed in magic? Then science gave us even more complicated answers to unanswerable questions?
Let's also review this next fact: the Gems are out of touch with humanity. Sure, they like to act like they know more but they seem confused about things like video games and sound equipment. Granted, Pearl built a rocket so that counts for something. It could just mean the Gems don't know about recreational human stuff and this point is moot.
But I wouldn't be typing this if I didn't have more evidence would I? You know your bro Evtini better than that. When Peridot showed up, the Gems were scared because of how advance her technology was. They knew nothing about it. Lapis (who had not been to Homeworld in thousands of years), claimed that the whole place had changed. Could it be that originally the Gems believed in magic but thousands of years of advancing technology made them abandon their beliefs in magic? They realized they weren't really magical beings because magic didn't really exist and because of that they became more advance. Of course, the Crystal Gems wouldn't know this and would still believe in magic. They believe their powers are magic, bubbles are magic, their weapons are magic, warp pads are magic, monsters are magic, they items they hunt down are magic.
Too bad for them magic doesn't really exist. Only a science they can't possibly understand.