What has happened this season that is arc related?
1. Dean stopped being a demon in ep 3. They've vaguely talked about finding a cure, but only did something about it in ep 14, which was a dead end (and Cain died). Now Dean says he's okay having the Mark, and Sam is broody.
2. Crowley's mother turned up in ep 7. She moved into Hell in order to manipulate Crowley to do ... something (possibly star in a daytime soap opera).
3. Angel Hannah - remember her? She hung around Castiel for the first three episodes, then went back to heaven in ep 7.
4. Metatron is still a prisoner, still being vaguely threatening. Has appeared in two eps this season.
5. It's occasionally mentioned that Cas's grace is running out.
The following looked like they might be important, but now seem like dead ends:
1. Cole turned up in ep 2 with a vendetta against Dean. Reappeared in ep 7 and turned to the good side. Special guest appearance in ep 15.
2. Castiel tracked down his daughter in ep 9. She hasn't been seen since ep 10.
If we hadn't seen Rowena before Hannah disappeared, I'd raise the possibility that Rowena is actually Hannah undercover for Heaven. Sadly, this idea is probably too interesting for the show as it is now.