NMEA might be better for debugging, meaning for the MNF development team. How many is that? 3, 5, 10? And users are only using NMEA if developers ask for it.
Comparing that to those tens of thousands (hundreds of thousands?) of users using gpx this should really be a no-brainer.
One of the reasons I became interested in MFN a few years ago was the fact that it offered NMEA-logging. So at least ONE non-develepment-team-member is using this feature. But nevertheless - I don't see any first or second option: There are two kobs, the first one "record as GPX", the second one "record as NMEA", and the options to save as NMEA or GPX automatically.
I must say that it is not a high-prio for me anyway, and based on what @mapper said: I assumed nmea was the "first" option and I did not even check (sorry).
However, when I look in Tools-> Recording is see that GPX is the first option (2.2.x versions).