I hope I'm not wrong, but I've always felt that the all metal and glass MF lenses from the MC era onwards pretty much could outperform an AF lens of a similar catagory (same era, or current) simply because physical tolerances are usually a lot tighter on the MF lens. I'm not sure about optical glass composition and coatings, but that might have an impact as well.
Things get a lot more complicated when you start mixing brands .. like I have.
What if you start pitching an OM 50mm 1.4 against an EF 50mm 1.4? Or a CZ YC 50mm 1.4 against a AF Nikkor 1.4? I guess if you rerally want to expand the comparisons, you could include medium format lenses, even though I've heard arguements that putting a CZ 80mm meant for a Blad on a 35mm body may not necessarily gain you sheer lpi as the medium format lenses were deisnged with a much larger film format (to compensate) and image circle in mind.
You can tell I just came in from too much time in the sun. LOL!