I suspect you want to know how they stack up as musicians/performers compared with each other.
Both are brilliant musicians, prolific in written and recorded output, organized several virtuosic ensembles, toured regularly, and were both lead guitarists of the highest order.
Prince has sold far more records than Zappa (by a factor of ~50x). This is because of three reasons.
First, Prince has a deep pop sensibility found in at least two dozen songs, perfect examples of traditional song craftsmanship and arrangement. The songwriting found on early songs “Why You Wanna Treat Me So Bad” and “ Wanna Be Your Lover” is a seductive blend of soul, funk, and rock that would continue throughout his career. This blend predates his fame and brings him many fans. While Frank’s songs were intricate and often peppered with elements of doo-wop, rock, and even some pop, his lyrics alienated most listeners. This lack of broader acceptance was despite songs full of fun and highly literate and clever lyrics.
Second, Prince’s timing with MTV and Purple Rain was a perfect storm for worldwide fame. An innovator of music videos (like Frank), Prince was a case of being in the right place right time. While it’s true, Frank’s fans might have been more loyal than Price’s through the years. This lack of popularity is because Frank was never as famous as Prince in terms of numbers. Ironically, Frank might be best known as a personality rather than a musician.
Finally, Prince’s voice is a great instrument. He could sing in all sorts of styles and had a beautiful falsetto. Frank’s voice served his compositions well, but he was more a talker/singer than a singer in the more traditional way Prince was.
That said, I find Frank a far more exciting musician and force in music. I listen to Prince now and again, but I always listen to Frank. I love his bands, the way he lets them all play, and his guitar work is highly underrated, IMHO. I don’t mind his singing. I’ve come to like it. Plus, he knew his vocals were limited, so he always had other singers in his bands.
Prince is akin to Paul McCarney, which might be a better comparison than Frank. But, to each his own. Respect Prince, love Frank.