I am persuaded that at least part of the perceived difference is due to retrofocus lenses having too many groups and too many air-to-glass surfaces. If on one hand it's indisputably true that multicoating greatly enhanced the performance of lenses with many air-to-glass surfaces (Zeiss' Planar, which was barely usable before coating was introduced, is usually cited as a paradigmatic example), on the other hand multicoating is not miraculous and should not be overused. All other sides kept equal, a lens that needs less groups by design has some advantage points in respect to a lens that needs many groups, whatever the engineers will do.
There are makes like Mamiya which in my opinion owe much of their success to the ability of their optical engineers to keep lens design as simple and as effective as possible, with a remarkably low number of groups.
On the other hand, however, there are also examples of extraordinarily good retrofocus lenses, like the Nikon Ai 28mm F:2,8 that I admire unconditionally and will never recommend enough.