Each of the story line's, other than Charlie's, made sense and was solid as a stand alone. Cramming them altogether into one episode that is the second to last of the series was a mistake. I don't even want another season, because I do feel like the show may have run out of steam on its own, but this season should have been 10 episodes. One of the reasons I believe that most shows' best seasons are their second and third is because they don't have to waste scenes explaining who characters are after the first season. Less exposition = better TV. Sopranos, Breaking Bad and Mad Men are all examples of this.
For example, Pruitt is an interesting character and I think the democratization of news is a really important topic, but by cramming Pruitt into 3 episodes and having Charlie inexplicably act like a complete idiot does the show and its viewers a disservice. Don's meeting with the girl in Princeton was fascinating if also incredibly uncomfortable to watch. That deserved more time. The NSA plotline with Neil deserves more time. The right of free speech vs. the need for national security has been covered before in other TV and movies, but is interesting nonetheless.
I feel like Sorkin is just dumping every scene idea he ever had onto the screen, no matter how disconnected they are. The scene with Will in jail was absolutely awesome and vintage Sorkin, but again, it was somewhat disconnected from the rest of the show.