Watched this today.
First and foremost I loved the cinematography. The framing of shots was spectacular!
All the acting was great and I enjoyed the plot (yes the new pope was predictable, but still).
I think it deserves its nominations.
However, I too kind of groaned at the ending. It just felt needless and actually hurt the story and the movie a bit. The movie was a good one on the politics behind power and was an interesting ride that held my attention the entire time. The tacked on twist just felt needless and should have been trimmed. All things must serve the story and the twist didn't serve it well. I will say it would have worked much better (to me) if it was just a straight up woman who they elected. At first I thought that was that it was and liked it, but the hermaphrodite angle muddied it a bit with no added point.. What point it served had already been nailed home without the needed twist.
Also I don't think it's anti-Catholic at all. We attend Catholic church but my daughter and I do silently protest at the end of church when they want us to read a prayer for vocation that they have printed in the back of the hymnal. Both our view is "Don't complain about needing more priests if you are ignoring half the population. Let women be priests if you need more of them!"