can probably be brought down to the fact that the of the second half of season three and all of season four were produced in their entirety before broadcast. For the first two seasons Harmon and co were able to gauge audience reactions and in tern influence how they wrote later episodes. With the hiatii all the episodes were created in something of an echo chamber and there was no way of correcting the course when things went awry.
One of the few episodes that showed promise this season was the Susan B Anthony Dance episode. Brie Larson's character interacted really well with Abed and it looked like they were building up her character for future appearances, and then nothing- she's not seen nor heard from again.
Another flaw was the lack of interplay with the secondary characters like Leonard, Fat Neil or Garret. All of them appeared in the background, but we never got an episode like Advanced Dungeons and Dragons or Competitive Ecology which gave them a chance to shine. Instead we got Alternative History of the German Invasion which re-used the annoying German foosball players from one of the lesser episodes of season 3.