The second season was directly teased from the first season. (I called a lot of the reveals of the second season assuming they'd be twists in the first season.) The problem with the writing in the second season was assuming enough people had read at least the Wikipedia summaries of the primary references they had cited directly and indirectly in the first season. Which is a tricky problem with "mystery box" writing in that you assume at least some of the audience will do the research, but you have to keep the show accessible enough for the people following the show but not the mystery solving / ancillary materials.

So far the promos for S3 make it sound a lot more straightforward with less "required reading", but we'll see.