I'm really surprise but face to face, in DPReview 'Image quality', the Pen-F has better sharpness and better contrast than the EM1 MKII.
The Pen-F certainly offers good image quality. But these are really small differences, and highly influence by the exact image processing applied, which is nearly impossible to normalize.
With a camera's JPEG output, it's a given that the basic image-processing choices are chosen by the camera's maker. But it's just as variable in the RAW domain, as each camera's output is shaped by the choices of the (in this case) Adobe camera profile for a given camera. The Pen-F may lead the m43 pack in raw IQ, but there may be other choices with essentially the same IQ that suffer from a bit less talented JPEG engine or camera profile choices.
The original E-M1 used a Panasonic sensor apparently to accommodate Oly's marketing imperative to incorporate PDAF sensors. And there's no doubt they compromise its long-exposure noise performance. And it's never matched the original E-M5 in the DPReview test shots. But nonetheless the difference aren't really field-relevant unless you do astrophotography. I'm really picky, but if I don't specifically remember shooting a shot I can't tell you which camera I used without looking at the metadata.
There is more required of an E-M1 class product because of Olympus' understandable desire for their flagship to be all things to all people. When you relax the requirements in the areas of PDAF support, C-AF function, video and general sensor readout speed it may be possible to produce slightly better IQ, as well as substantially increasing the number of sensors to choose from as many more will meet the general specification required.