The only thing MF now has a big advantage/difference is in the way they work.
I had a H4D-40 for almost two years, and I can say that the leaf shutter lenses alone are a big reason for using MFD. I've tried everything to get the same high speed sync on nikon/canon systems with no luck. The 35mm "solutions" are no practical at all (ND filters, Canon/nikon flashes, HSS transmitters etc etc).
Yesterday I was doing a shot in the afternoon and I wanted a shallow DOF look with strobes, I was using a 5D mark II, ISO 100, 1/160, f/11. With the H4D-40 I could've made it happened with ISO 100, 1/800, f/5... and f/5 DOF I something like f/2.8-3.5 in 35mm. Of course getting a wider DOF in MFD it's harder.
- Also true focus It's so much faster than a multi-point AF sensor, it really works, made my life simpler.
- Another clear differentiator is how they render color, I really hate canon magenta tint on skin tones, but of course you can fix it in post or with something like colorchecker passport, but getting a natural/real color from the beginning it's a time saver.
But LR4 is a game changer for me, you can recover the highlights and shadows in a more pleasant and natural look, I feel like my 5D mark II suddenly had a dynamic range update