Did I miss something? Only 6 episodes in season 3?

nope 6 episodes in season 3 but to be honest the first 5 were not as good as the other 2 seasons the first was good on boston but then this whisteblower thing went on a bit last episode was good tho liked the band jam

Sorkin seemed to have lost interest in the show during or after season 2

The show was sort of semi-cancelled. You have to admit we got a dozen episodes' worth of plot, though, crammed into 6, unfortunately often without heads or tails (Neal gets to come home but not Glenn Greenwald or Laura Poitras, hmm.)