I've done the comparison between the 528 CF and AFi-ii 12 (Aptus 12) and the AFi-ii 12 vs CF 39MS. I have managed to perform all the the tests using the same lens eliminating that as a variable.
Here's a summary of my results:
CF 528 vs Aptus 12 CF wins easily in detail, color tonality and DR in microstep mode, loses in convenience. If you shoot say a couple peaches, apples or grapes with both, you'll easily see how much better the microstep files are in terms of color and tonality. Areas that look just like one color with the single shot aptus 12, have all kinds of fine texture and shades in the microstep file. In single shot mode the aptus 12 / IQ 180 obviously will record finer detail, however the 22mp backs do get more dynamic range and have a grainless file at base ISO unlike the 80mp dalsa chips. Color? The purveyors of the new backs say its improved... I haven't scientifically tested this, but the older 9um backs have a great look.
CF 39 MS vs Aptus 12 Too close to call on fine detail when CF in multishot but maybe the Aptus 12 edges out. Obviously in single shot mode the CF is beaten by the 80mp backs but again the differences are not as large as one might expect. CF 39MS has more DR by about .5 to 1 stop in single shot mode, and 1.5 to 2 stops in Multishot mode.
I think of the CF 528 in microstep as the best back I have ever used or seen. But its a limited set of applications where you can shoot microstep. I'm lucky to have both to use.
In general all the above really compares the situations where multishot is applicable - art reproduction, food photography, product work, still life, etc - its not going to work for everything. The really great thing about the modern 80mp backs is how versatile they are - getting close in a single shot, and one can shoot at higher ISO's. But still for ultimate quality in a static scene, the microstep backs are very hard to beat.