Actually, Fr. Ripperger explains JPII's method in this article. It is called the Hegelian dialectic. In this case, Thomism, is the existing element or thesis. It is opposed by Phenomenology, the antithesis. The synthesis of the two represents a new thesis which is an advance over the old (Thomism).
The whole problem with the pope's method is that it embraces the modern philosophy of Hegel.
Perhaps his work, which has been around for over twenty years, is still largely unexplained because it is utterly unexplainable.