I have spent two days chasing down what the cause of the focus/ sharpness issues could be. Initially I believed that it was auto focus accuracy as did/do many others, but that is not what I found except with a few lenses (and very slight). Mostly it comes down to technique and execution of the capture. CURE: Faster shutter speeds Smaller f-stops
With the higher resolution of the sensor it will reveal with less mercy softer shots due to shake, soft focus or shallow DOF. I shoot with a high rez MF back and you really have to stay on point to get the most out of any imager as pixel count increases. I have found even with good FX Nikon (zooms and primes) that the old f2.8-f4 just won't cut it... you really have to move up to 5.6-f11 keeping an eye on diffraction limitations of each lens.
On a tripod you may have some benefits shooting in the Quiet Mode where the mirror comes up, pauses and then the shutter trips. Haven't tried that, just a thought.