I'll note that within the last 10 years at least four pro-level MF bodies have been available.
The Nikon F3HP was discontinued in 2001, as was the Pentax LX. The Contax RTSIII was also discontinued around then, and the Leica R9 is still available new. All are pro 35mm MF bodies.
Personally, I suspect that 1/250th flash sync did in the old pro bodies as much as AF did. Certainly in Nikon land, going to an F4 from an earlier F gained you fairly massive improvements in the flash system (Wider ISO range for TTL[against F3], 1.6 stop higher flash sync[2 for an F, 1.6 for F2 and F3], distinctly improved flash metering, standard ISO shoe), not to mention integrated winder/drives (why was there no winder for the F3? only the MD-4 drive that is overkill for most applications, the F2 had the nice, lighter MD-3) and vertical controls. And metering improved as well between the AF pro bodies and the earlier MF pro bodies(spot metering, matrix metering). While later MF bodies got a lot of the improvements that the AF pro bodies did (the R9 and RTSIII are closer in form and capability to an F4 or EOS 1 than a F3 or New F1) they were never mirrored in the more popular systems.
As to medium format, I'll note that the three most common systems today (sold new) are all AF or AF capable 645 systems (Hassy H series, Mamiya 645 AF, Pentax 645). AF 645 systems have come to dominate the MF market, at least for new sales (used is dominated by the older 6x6 and 6x7 systems that are difficult to impossible to get new these days, aloong with dirt cheap older manual 645 kit)