The optical quality of the optics in the AF sensor module could be enhanced, better glass and coatings, I believe it is plastic now.,,, would have a huge impact on reliability and precision, and an extension in size so better than 2.8 would be possible would help 1.4 lenses greatly, f/2 as well,,, larger sub mirror,,,
Marianne Oelund has quite interesting observations reverse engineering the module,,, on DPR.
She also states that it is highly likely that an extra check and fine adjust is happening in the new/later cameras for AF-S,,,