This question has been covered in past threads, this one fairly recently was answered in great detail. I recommend all the answers given there.

In short though, you're working off the idea that the popes named John chose to name themselves after John the Evangelist, but that's not the case. Popes who renamed themselves tended to name themselves after previous popes, not after any other figures. The first pope to change his name was John II in 533, who felt that his given name was inappropriate (Mercurius, from the Roman god Mercury), so chose to take the name of his predecessor, John I. John I, and the 52 popes that preceded him, all used their birth names. Francis was the first to buck this trend since Lando in 913.