The FFT method is fast but carries several premises: an f-number large enough for scalar diffraction theory to apply, the region where the point spread function has significant energy being small compared with the distance from exit pupil to image plane, the exit pupil not being greatly distorted relative to the entrance pupil, and sampling fine enough to represent the point spread function. For systems where the exit pupil is greatly stretched, switch to the Huygens method.
The Huygens method is not based on an FFT. The only premises it needs are an f-number large enough for scalar diffraction theory and sufficiently fine sampling. Use it for tilted image planes, greatly distorted exit pupils, arrangements where the chief ray cannot be traced, and summing across several configurations. The geometric method is an approximation to diffraction MTF and works where aberrations are large. Once the wavefront error exceeds about 10 waves, switch to the geometric method. It is also the only method that can include the loss of contrast from surface scattering.