I have both. The basic difference is the MK is the gold standard that everything else has been judged by for several years now, there isn't much out there that has the same feature set and is inclusive of advanced software functions like waypoint routing for no additional cost. Some flight controllers now have similar software features but as steep additional cost add-ons, if all of the advanced functions that Mk has are what you're looking for without spending just as much again to get those features then it's the only real choice.
H/F on the other hand does not have nearly the functionality that MK has and costs nearly as much. The big advantage is that you don't need to assemble any components onto boards or do any real software setup and configuration beyond the few steps of initial setup, it's very easy for just about anyone to make one fly. Mk on the other hand requires much more advanced skills to get in the air and is not for everyone, especially if you don't feel comfortable doing soldering work.
As far as basic flight capability, they both do autoleveling, altitude hold, and support just about any frame/motor configuration you might care to use. H/F allows auto leveling to be turned on and off, Mk defaults to on all the time although it is possible to turn it off in the software if you really want to, I've never done it. From my experience the autoleveling is about the same on either, Mk has the advantage with altitude hold allowing either fixed or variable height control which works quite well either way.
Adding full navigation to either one is additional cost, the H/F needs a $450 GPS add-on board, MK requires a navigation board plus GPS board, the total cost of both being a bit less than the H/F setup. Functionally there is no comparison, MK wins hands down in the GPS category, the functionality and feature set is years ahead of H/F and it all works although some of the advanced capability can be a lot of work to get setup the way you want it to work. Basic functions such as position hold, return to home, and waypoint routing work flawlessly on the Mk and I use it on all of mine. Capabilities such as keeping the camera pointed at a POI (point of interest) are included but I have yet to use it, and other things such as carefree mode that keeps control response the same (tail-in) regardless of orientation are nice when starting out but again not something I use. H/F GPS is basic functions such as position hold and RTH and that's about it as I recall, so dollar for dollar you get a lot more from MK on the GPS side of the equation.
One other thing, the H/F works with standard PWM ESCs, Mk requires I2C controllers. The Mk versions are roughly $75 each and you need one for each motor, so depending on configuration that can add substantial cost to the initial buy-in if you go the MK route. On the other hand, the Mk hardware works seamlessly where I've had some issues with H/F not playing nice with some cheap ESCs from China, or the ESCs not playing nice with the H/F, however you want to look at it...
So if features and functionality is the primary concern you may want to consider going with MK being aware that it is a more complex system and likely more expensive in terms of hardware. If simplicity of build and setup along with initial cost is a bigger concern you may want to go the Hoverfly route if you don't need all the features and functions that MK provides.
Ken