Skies of Arcadia or Star Ocean 2 for me.
Not really sure how Mass Effect counts but Star Wars doesn't. Both rely on a healthy amount of dubious space magic to connect the dots, it's just that the Mass Effect series has 90 hours to also explore everything from AI to the singularity, sentience etc whereas the films don't. The KotOR games offer a similar amount of sci-fi side-topics explored across dozens of hours, and even the films depiction of a totalitarian empire with planet-killing weapons, and whether resistance is meaningless or futile, is hardly a 'non-sci-fi' topic, even if space wizards is.