I upgraded several years ago from a 645 Pro to a 645AFD3. With the Pro, I mainly used the 45mm f/2.8 and the 80mm f/2.8 lenses. Now with the AFD3, I use the AF-D versions of the 45mm, 80mm and the 75-150mm. The AF-D lenses are a step up from the AF (non-D) lenses wrt build quality as they all have a metal barrel instead of polycarbonate for some of the AF lenses. The manual focus N lenses, I used with the Pro, are also metal. But I believe the optical design of the 45mm and 80mm f/2.8 is the same for the N (manual focus), AF and AF-D versions. The coatings were supposedly improved for the AF-D lenses. If I look at my prints, I can't see much difference in image quality. But I've never done any comparison shots of test charts or brick walls. I only shoot BW negative film with the Mamiya. My standard print is a 25 x 33.5 cm image on 11x14 inch FB paper and occasionally a 40 x 50 cm print. I'm happy with the image quality I get from the Mamiya lenses.
For the OP; it comes down to whether you want the extra features of the AF system or save a bit of money with the MF system. I appreciate the autofocus, the higher shutter speeds, the exif print on the film edge and the 75-150mm zoom with the AFD3. A little warning; the Mamiya/Phase-One/Schneider-Kreuznach
AF LS leaf shutter lenses do
not work on the AF/AFD bodies. The manual focus 645 lenses can be used on the AF bodies but only with manual aperture. I use the 50mm shift lens on the AFD3.
You can find lots of Mamiya (and other) camera manuals, brochures and reviews
here. Digital back compatibly
here.