Then forgive me for being silly - but was it not Phase that charged a premium price for an old Russian lens that had some, to say it kind, personality in regards of even sharpness??
My feeling on that endeavor was that there was optimism that a select number of quality lenses could be pulled form a large purchased batch, modified to bring the most out from the lens (with a digital back), and then be a quality alternative for tilt/shift. As that process unfolded, it was becoming apparent (to me) that the results were not where Phase One hoped to get them, despite only working on the very best copies. And while the $3,999 price vs previous $800 price seemed like a money grab, I don't believe it was as simple as just buying $800 lenses and marking them up to an obscene price. The process of testing and working on the products and (especially) the likely amount of lens waste that simply wasn't even up to the task of being a candidate for that process played a significant role in the pricing. When it became apparent that the lenses weren't cutting the mustard despite best efforts, there was a notable decline in the emphasis put on that lens as a viable solution (at least in the US).
As far as improvements on D lenses vs older Mamiya AF/non AF lenses, some lenses improve a great deal, others not so much, in terms of sharpness. What I have seen more widespread are improvements in chromatic aberrations on the newer lenses, even when there wasn't a significant sharpness increase. Some of the older Mamiya glass is very good, in terms of sharpness. Little difference, if any, is noticeable between the 120mm. The 45mm was modestly improved in sharpness, more so in CA correction, and in general, the build quality from all the lenses is significantly improved, and the warranty extended from 1 year to 3 years. On balance I don't see any highway robbery being committed. The last published price of the original 45mm AF was $1,332 and the introductory price of the D version was $1,890. Not an unreasonable difference.