Those differences can be down to:
Lens, ISO, aperture, raw-or-jpg, picture style and sharpness setting, noise reduction, processing software used.
Out of them, i'd presume raw/jpg and sharpness setting would be making the biggest difference of them.
To control variables, you can mount an EF-lens on a NEX via an adapter, use DXO or something to process both shots with the same noise-reductions etc.
But some variable you can't control, like just because the camera says iso100 doesn't mean it's actually iso100, and picture-styles are going to be brand- and probably even sensor-dependent.
I'll be waiting until DXOMark does their nex7-review before passing judgement.