The problem with focus stacking is that, in most lenses, the focal length, and, thus, the magnification, changes as the focal plane changes, sometimes quite dramatically. You end up with a set of images that don't line up properly. I've tried it with long lenses for landscapes, to avoid having to stop down to f/20 for sufficient DOF - the results weren't worth talking about.
So far, I haven't been able to find a list of lenses where this effect does not occur, especially at the pixel level.
I suspect that the future solution to focus issues will be software-based deconvolution, likely combined with sensor oversampling to increase the data quality, rather than anything in lens design. Same thing with wavelength dispersion and diffraction-related loss of sharpness.