I think different readers will see different moral lessons from Mark Twain's The Prince and the Pauper. Various readers will see different lessons because of individual backgrounds, but I do believe the book portrays some universal morals to readers.
One moral lesson of the book is not to make initial snap judgments about people based on rudimentary, surface-level knowledge. The phrase "don't judge a book by its cover" is a good synopsis for this concept. Both Tom and Edward believe the other boy is a certain way and has certain advantages, but after they switch places, both boys realize their initial notions were incorrect. This kind of moral lesson shouldn't only be applied to socioeconomic status, either. It could be applied to religions, ethnicities, and political affiliations.
Another moral lesson found in the book is the same moral lesson Spiderman's uncle teaches him. Peter Parker's uncle famously told Peter Parker, "With great power comes great responsibility." That's exactly what Edward learns over the course of the novel. Between Edward and Tom, Edward is the more dynamic character because he changes from being rude, obnoxious, and selfish into being much more selfless and humble. Once he finally gets his original place back, he uses his power for good instead of selfish gain.
Mark Twain's The Prince and The Pauper tells a story of Edward (Eddie) Tudor and Tom Canty. During the story, the boys trade clothes in order to escape from their own lives. Each boy learns an important lesson during his life as another person.
There are multiple lessons (or morals) which can be learned by reading the novel. First, one must never judge a book by its cover. Each boy has his own thoughts about who the other is. By walking in the shoes of the other, each learn that their life is not what they made it out to be.
Another moral lesson of the novel speaks to is to never abuse one's power. Since the novel possesses one point of view from the elite, the novel illustrates that power should never be abused.
One last moral of the novel illustrates the fact that there are both good and bad in everyone's life. "We" must accept our lives for what they are and make the most of them. "We" cannot allow our coveting of another to rule life.
Mark Twain himself would probably have been quite uncomfortable about the notion of drawing simplistic moral lessons from the story. In certain ways, this work satirizes concepts of both the inherent nobility of the poor and of the rich, and avoids sentimentalizing both class and childhood. Instead, both young boys, like Huck Finn and Tom Sawyer, are a mix of good and bad, acting out of both kindness and self-interest.
One point the book does make is that much of how people regard us depends on our situation in life; Twain is frankly egalitarian in his social vision, deflating the notion of the superiority of the British aristocracy.
Another major moral theme is one we see in the coming of age of Edward, who as he matures, sees that being a king is not just a matter of having power and privilege but also of assuming responsibilities and obligations.