I think I experienced season two with a bit of Star Wars prequels syndrome. The big reveals in season one where a masterpiece of story construction; complex ideas presented in simple ways. Season two for the most part has struck me as being heavy on plot in order to create different kind of character reveals because they know they can't match the (okay, thrill ride) reveals of the first season. Yet there's so much lip service paid to the first season, that you can't help but refer back to it. They reference three mile island and Thatcher and set this grand extermination in motion, but it's just variation in the big reveal at the end of the first season.
I was also a big hot stressed out mess when I was watching most of the episodes and out of town for the others so maybe I just need to take a rainy day and marathon the whole thing again.