We demonstrate an enhancement of the plane wave expansion method treating two-dimensional photonic crystals by applying Fourier factorization with generally elliptic polarization bases. By studying three examples of periodically arranged cylindrical elements, we compare our approach to the classical Ho method in which the permittivity function is simply expanded without changing coordinates, and to the normal vector method using a normal-tangential polarization transform. The compared calculations clearly show that our approach yields the best convergence properties owing to the complete continuity of our distribution of polarization bases. The presented methodology enables us to study more general systems such as periodic elements with an arbitrary cross-section or devices such as photonic crystal waveguides.