what is the philosophical problem that arises in the end

Huxley does not reveal why Mustapha decides to keep John as part of an ongoing experiment, even though he willingly sends other misfits within the society like Helmholtz and Bernard to an island. One possibility is that Mustapha views John as a kindred spirit via the Shakespeare that they have both read. He keeps John because he wants to convert John into rejecting Shakespeare and into accepting civilized dogma. However, as the ending shows, accepting society implies giving up John’s individuality, and Mustapha’s experiment fails.