I was listening to Chris Carter on the Nerdist Writing Panel, and he talked about how the original series was written. One of the writers would be in charge of the episode, but it was a collaborative effort when it came down to pitching stories and the editing process, including Carter rewriting scenes if he felt it necessary. This time around, there is no writers' room. Each episode is written and directed solely by one of the original writers (Carter for eps. 1, 5 & 6, James Wong for 2, Darin Morgan for 3, and Glen Morgan for 4), though obviously they have some collaboration over the season's theme (which is basically why William is mentioned every week).
I think that explains the quality of this season. While it sounds like an interesting idea to give some of the X-Files' original writers full control, it also makes for a very disjointed season since there isn't anyone to reign them in when needed. That, and the writers who got to direct their own episodes don't have much directing experience at all (Darin only directed 2 episodes of Millennium nearly a decade ago), which I think results in some of the weaker acting we've seen.