I'm not averse to the changes in the GDF standard you propose. I think now that yt-3.0 is incorporating units as cleanly as it is, this makes sense to allow the format to specify an arbitary unittype instead of requiring cgs, since it can be so easily modified within current/future versions of yt.
I honestly don't know how many people are using GDF, but it seems like these changes would break backwards-compatibility. Is it possible for us to retain that compatibility by automatically running "field_to_cgs" on GDF files which do not possess the HDF5 attributes specifying the units? Or perhaps since yt is the main source of GDF files, we can just move forward without having to worry about too much backwards-compatibility issues?
Anyway, this seems like a positive change. +1 to continue on this.