The coupled wave theory dealing with optics of discontinuous two-dimensional (2D) periodic structures is reformulated by using Fourier factorization with complex polarization bases, which is a generalized implementation of the fast Fourier factorization rules. The modified approach yields considerably improved convergence properties, as shown on an example of a 2D quartz grating. The method can also be applied to the calculation of 2D photonic band structures or nonperiodic cylindrical devices, and can be generalized to elements with arbitrary cross-sections.