I am the owner of a 4-16 ATACR with the mil-c. I bought it recently, just before the release of Leupold's PR1 reticle. Had this reticle been released sooner, I probably would have gone with the mk5. Thus, right now I am thinking about flipping my ATACR for a mk5 5-25. But to answer the OP, comparing my 4-16 F1 ATACR to a buddy's MK5 3-18...
Both:
-Have the locking "Zerohold" locking button on the elevation turret. A small thing, but I love its simplicity. Wish all scopes had them
-Offer 0.2 mil subtension reticles. Only recently with the MK5 on the release of the PR1 mil. This and the NF mil-c are up my alley
-Track well. Both have been super reliable and true-to-track thus far
-Have perfectly fine glass. One doesn't outclass the other, and I can't tell a difference between their image quality. However, I have not looked at their low-light performance's side-by-side. For scopes, both are good, but in the end neither one has better glass than a spotter or pair of binos that cost half as much.
NF wins:
-The image at 16x in the NF looks better/bigger than the picture in the mk5 @ 18x. It is difficult to describe in words, but with the NF you are "sitting closer to the TV". IMO it just feels like more magnification at 16x than the mk5's 18x, and an altogether better picture. It is only something one would notice when looking through each one side-by-side. But the NF is a clear winner if you do.
Mk5 wins:
-Leupold owns the patent on the zerohold elevation button. This means ONLY the 4-16 NF has it because it was released before NF was sued for it (i think). All mk5 models have it. Not a big deal if you are only considering between the NF 4-16 and the MK5 3-18.
-Mk5's are lighter. I could run a mk5 5-25 for the same weight as my ATACR 4-16. I'm a glutton for counting ounces even though my rifle is 15 pounds, so take that for what you will
-Less expensive. It is reasonably priced, and can be had for several hundred dollars less than the 4-16 atacr. When comparing the 5-25 or 7-35 models between the two manufacturers, the mk5's look even better.
-Magnification is changed without turning the entire eyepiece... The lens caps on my ATACR cover up my bubble level at low power lol
Conclusion/TLDR:
-Between the mk5 3-18 and 4-16 ATACR: I like my ATACR better.
-Between any mk5 model and the 4-16 ATACR: I will likely buy a mk5 5-25 in the near future to replace my ATACR for the observations stated above. I'm really in no rush though, because this ATACR is nice.
-Between mk5 and ATACR in general: For me the mk5 wins because of their recent release of a reticle I like, they're lighter, they're less expensive, and have the zerohold locking button for all models. The optical and tracking performance between the two is really SO CLOSE that the button, reticle choice, weight, and cost are the major deciding factors. Since I have no experience with higher power models, this assumes that optical quality remains the same for the 5-25 and 7-35s for each manufacturer, respectively.