We wish that we had something really deep and insightful to tell you, but the title of The Prince and the Pauper is about as simple as you probably imagined it was. There's no secret meaning. No metaphor. There's just the fact that a prince and a pauper are the main characters of the novel.
But why does Twain call it The Prince and the Pauper, instead of Tom and Edward? Well, the novel isn't really about them; it's about their about their socioeconomic statuses, and it's about how unjust the divide was between the rich and the poor during 16th-century England.
While we totally love Tom and Edward, the story would be the same with any other prince and any other pauper, and that should tell us something: this story take place in 16th-century England, but it could happen anywhere there is a divide between rich and poor. Tom and Edward just happen to be the most convenient vehicles for the social critique Mark Twain wanted to write.