Supernatural has never been a show to shy away from tough topics or portraying the gray line that always exists between good and evil. Angels have been portrayed as selfish and powerful creatures that would just as soon destroy the planet as save a cat in a tree.
There have been a few good eggs and we came to realize that while there are some bad, there are also many others like Castiel that want to look out for the human race. After the death of literally thousands my evil Cas, it appears the angels are taking a cautious stance with Naomi seemingly as the ring leader.
The angels have always kept their true intentions pretty close to the vest. I can't help but wonder that the endgame is for them and what part Sam, Dean and Cas play in it. We've seen other angels pop up occasionally, but always in minor roles and acting more robotic than anything else.
Naomi is one of the few that actually seems to show some real emotion, but I am still not even sure if she's actually an angel. She does have the ability to control Cas and apparently keep him out of heaven. She also pulled him out of purgatory, so that makes her kind of high up on the food chain. As the mid-season finally wraps up and the next episode that premieres in January seems back on the angel/ demon story line.
I admit that this season is thrilling and I can't wait until I the new episodes come back in January.