Now that you mention it, I own a Nikon D800 (full-frame, 36MP) and the raw files it produces do not look as great in ACR as the ones my Fuji XE-2 produces, which only has an APS 16MP sensor, yet it produces outstanding shots almost every time.
However, when I open the Nikon raw files using Nikon's Capture NX-D, they suddenly look awesome. I'm guessing this means some kind of codec incompatibility, or something along those lines and have been asking Nikon about it , but I have not received an answer yet.
I'll keep you posted if I learn anything (and please, if you find anything, let me know).
ML