The biggest argument against the Four Sword is the intro to Four Swords, as Vaati (Who is usually considered weaker than Ganon) was able to break free without any outside interference. Sure, Ganon jailbreaks the MS in WW, but he had to assassinate the Sages to weaken it if I recall. And as many others have said, you can't fairly compare the Phantom Sword and the Master Sword since the Phantom Sword has barely any screen time even compared to the Four Sword. An argument for the MS is that it is perhaps the only one of the three that is truely divine, having not only been crafted by the ancient Sages but also wielded by Hylia, then imbued with three Sacred Flames by Link before finally being given a sacred blessing by Hylia, the final of which is purported to have bestowed the elements it shows in games like OoT. It also, early in the child timeline absorbs the Sol, a Sacred Light from the twilight realm.