Transfigurations at least has a consistent main theme and message, and bad as the final special effect is (my dude I can see the texture on the zentai suit you're wearing) the resolution and the way it unfolds are very Trek, especially the semi-hopeful note of "they're jerks but only because they're ignorant and they might change once they know better." It's easier to forgive a lot of the awkward stuff in the middle when the end is on brand.
Meanwhile, Sub Rosa's only message seems to be "ain't no fuckin' like ghost fuckin'."
Also, I maintain that Code of Honor is the worst episode of TNG by far. Even discounting the uncomfortably possibly racist undertones throughout, the whole thing is full of incredibly regressive and outdated stereotypes of gender even for the time. Also it's just kinda boring.