I think they both work well on girls. Yes,
Aubrey is originally masculine but I think it's kind of silly to call it a boys name these days. It's in the top 20 for girls and
Aubree is in the top 100 so while it was originally masculine it sure can also be called a girls name by now or at least a unisex name.
I love them both. They make me think of autumn which is my favorite season. Of clear, bright skies and colorful trees. I love that image. I imagine an
Aubrey to be a little more wild and outgoing and an
Audrey to be more elegant and calm. I love the meanings of both names as well as their sounds.
At the moment I'd choose
Audrey. It's just not as common and less likely to sound dated. I also dislike how so many variants of
Aubrey are being used.
Aubree is in the top 100 and I've seen
Aubrie, Aubri and Aubry. I've never seen
Audrey in a variant spelling in real life. So that is a plus. Also
Aubrey is just too common for me right now. I hope it will lose some of its popularity soon but it doesn't look like it will. I also love
Autumn, by the way.
Oh and
Aubrey and
Audrey don't have much to do with each other except for the similar sound. They are completely different names with different origins and meanings.