The first season was able to play with time and setting in laying its mystery out, while Season 2 turned into more of a faction-based creature feature.
That would be an understandable reason why Season 3 was taking so long to develop.
Because it took so long to put Season 1 out to audiences, many of the actors weren’t able to return in full, or at all, so quite a few narrative jumps were necessary.
And even that was a major hassle, since the first season adapted all three books inBlake Couch’s novel trilogy, leaving no major pieces of source material to draw from.