dev is a "parent" of 2.0 with only a two commits apart, so it's really only the latter we need to concern ourselves with.
It seems like the brunt of the changes* are renaming packages. I believe it would be convenient to slip these changes in at the same time as the Flixel v2.57 renames are taking place.
* ...that sounds wrong; I think I'm mixing up two different expressions, but I can't figure out how it's supposed to be.