The answer is simple, and to explain it I will quote Yogurt from Spaceballs:
"Merchandising! Merchandising!"
If Disney used existing characters from classic video games as the protagonists, they would have to share/pay substantial licensing fees to the companies that own those characters when they try to sell toys and other items based on those characters. By creating new characters they can not only tell an original story without any preconceived notions the audience may have about the characters, but they also get 100% of the merchandise profits.
A similar situation occurred with a movie many critics are comparing Wreck it Ralph too, Who Framed Roger Rabbit… though in that instance Roger, Eddie and others were original characters in the novel that the Disney bought the rights to and adapted into the final film.