The finale just reinforced what I've been thinking since they killed Arden. The show only had one solid story and that was the saga of bloody face. Everything else was padding that they had no way to end which they rushed out of the way and Jude seemed to have been kept around out of contractual obligation to Jessica Lange to get her on next year's Emmy ballot
The EW post-mortems with Murphy have been very telling in that regard.
"Lana really emerged as the heart of this season. Did that evolve? Or did you like Lana’s story as it went on? Or was it Sarah’s performance? She did really become an important part of the story.
She did. When I pitched this season, the original final episode was all just going to be Act One. It was gonna be a longer version of that. The original finale was gonna be Sarah Paulson now free, a Jacqueline Susann/Truman Capote type, gets a kick in her conscience from Kit and goes back in and shuts that down. And we were gonna have the whole last hour be a documentary of her doing that. But I think when we were working on that I thought “I don’t want to see feces smeared people for an hour. It’s so grim.” So we abandoned that around episode 10. We thought let’s give Jude a happy ending. Let’s make that one act. But let’s really make the last act Paulson vs. Bloody Face. So we broke that out early on but kept the original idea. I was thrilled with the changes. I was very thrilled with how emotional it was. Some of that was John Landgraf who felt very strongly that Kit needed to go back in and get Sister Jude out not for himself but for his children. That dialogue was all sort of John’s that I thought was very beautiful. Tim [Minear] did a breath-taking script. It just all came together."
In an earlier interview Murphy said that one of the clues to the aliens was that they only appeared after Kit had sex. Well, we can see that was totally irrelevant in the direction the show went with that. The latter half of this season was one of the most obvious "making it up as they go" examples I can think of.
The show started whacked and crazy but ended in a fairly safe and predictable fashion. I'd have been happier with a finale that made no sense but did go out in a bizarre and bloody style.