I found this quote in a Playbill article. It comes from Prince's book, Sense of Occasion: "Phantom’s metaphor was omnipresent for me. I’d always wondered why in the presence of deformity our atavistic response is to pull back, perhaps not in horror, but instinctively. And then, if we are sentient human beings, we quickly realize how irrational that response is. Years ago, when I was in the Casbah in Algiers, a leper shook my hand, and I recoiled. Then I was with George Abbott in Havana when he told me that the manager of the Tropicana was a leper who was missing fingers, and I shook his hand timidly. I shared these memories with the company on the first day of rehearsal, and I have continued to say it to new companies ever since. It is for me the reigning metaphor of the show, the concept that gives the show its human focus and along with the romantic theme supplies a good part of the power it continues to have for audiences."
Of course, he has done just-for-fun shows, like On the Twentieth Century.