I think most of them had to do with the mother, who was much more a caricature in the first episode and the rest were over Fillion being his over-the-top self, both of which were toned down slightly in the second episode and what was still over the top was more in balance with the rest of the episode since, as you say, the second mystery was better constructed (and less obvious) which took some of the focus off them being over the top.