I've never tried any of the medium format AF cameras, but using AF with many 35mm SLRs and DSLRs I've found AF to be unreliable. I get too many slightly misfocused shots with AF.
I used several AF 35mm SLRs for years, and loved it. Then I found myself shooting more and more in situations where AF didn't seem to work well, and I could tell my manual focusing skills had deteriorated. After switching back to all manual focus I noticed fewer slightly misfocused photos. Sure, I still screw up, but it annoys me less to blame myself for trying, than to wonder if I'd have nailed the focus when I let the machine try it. For the subject matter I usually shoot AF isn't a neccessity anyway. Every subject that people say requires AF was photographed extensively for decades before AF. There is no doubt that AF is very useful to many photographers, but it is almost always possible to get the job done without it.
From most reviews I've read, AF on medium format cameras has been slower and clunkier than on pro 35mm systems. Maybe it's gotten better? Then again, my fairly recent Canon 20D has lousy AF; much worse than the AF on my Pentax ZX-5 (circa 1997?). I haven't owned a lot of AF cameras. I suppose it's possible that I've just been getting lemons.
I don't choose cameras based on whether they are AF or manual focus, but when using an AF camera I switch it to manual focus. I think most people prefer AF, but if there was a manual focus model with the same features as the AF model (other than the focus), but for a cheaper price, I would buy the manual focus model, because I have no need of the AF.
If I found that I couldn't manual focus better than my camera could auto focus, I'd go back to AF. So far I feel that I'm getting better results using manual focus.