The last time I tried to compare MPC-HC + MadVR and Plex, I had a really tough time telling the difference. This is with a calibrated Pioneer Kuro krp-500m and coming from someone who is is very sensitive to picture quality and video processing. Maybe if I tried again I might notice the difference, but at this point ease of use has become much more important to me. This is basically all with straight 1080p blu-ray rips. MadVR might be more useful when you need to upscale and deinterlace.
Basically, if set up correctly, the PQ differences between these programs (at least with 1080p content) is very small, and I'm sure most people will never notice the difference.