Neither GPS is more accurate than the other, they're both about the best I've owned and flown with position hold working like its hanging from a rope and the RTH autoland usually being within a couple feet of the takeoff point if not closer.
As to which one is better depends on what you want to do with it, I had two WKM and three Naza, I sold one of the WKM to buy the 3rd Naza plus some other goodies, I just don't need all the "features" that have been added to the WKM. Besides that as far was waypoint flying and all the other bells and whistles, I have a couple Mikrokopters that do all that and then some and the cost is free unlike the WKM where DJI charges ridiculous $$$$ to license the ability to do 5 or more waypoints. Granted they aren't distance limited like MK but on the other hand you can't realistically fly all that far on the onboard battery power so the distance thing doesn't mean all that much on a multirotor IMO.
For basic autolevel, altitude hold, and GPS functionality either one is an outstanding performer although I think the GPS works a bit better on the Naza, it's certainly faster to get a satellite lock than the WKM is. For the price difference unless you really have a need for the advanced functions of the WKM, save yourself $700 or $800 and get the Naza with GPS.
As for flight characteristics, if you were to fly each one through FPV goggles on the same type frame without knowing which was which you wouldn't be able to tell the difference if each one was properly setup, so spending the extra cash for the WKM isn't going to gain you anything there.
Ken