One of the things that impressed me when I first watched a trailer for Persona 3 was the bizarre and disturbing imagery associated with the Dark Hour, Tartarus, and the Shadows. The shutting down of all electrical devices, the eerie green glow, the red splotches that look like pools of blood covering everything, the blurring effects, the surreal tower of Tartarus rising up amidst a terrifyingly quiet city, and most of all the unsettling effect of Transmogrification in which every normal person is turned into a coffin... The images of the Dark Hour are very powerful and work incredibly well to transform an ordinary-looking town into a nightmare world where monsters roam. The city during the Dark Hour is one of the most ideal backdrops for a secret battle against a terrible, inhuman enemy that I have ever seen. The only problem with this imagery is that it just isn't seen often enough.
With a setting as perfect as the city during Dark Hour, you would expect the game designers would make as much use of it as possible, but instead I think I can count on my fingers the number of times you actually see that imagery across the length of the game. As far as I can recall, you only encounter Transmogrified people in two full moon missions, the opening movie, three or four plot events (including one animated cinematic), and the "end of the world" sequence at the end of the game. You only see a good exterior image of the tower of Tartarus two or three times. You are never even given a chance to actually wander around the town during the Dark Hour. The images of the Dark Hour are incredibly important to the themes and story of the game, but far too often these are simply glossed over.
One major symptom of this effect is the fact that it sometimes feels like the Dark Hour isn't very dangerous in of itself, even though the Dark Hour is the great problem that the heroes are trying to eliminate. I think this is mostly caused by the fact that the Dark Hour doesn't even seem to exist unless the player chooses to go to Tartarus or a plot event happens during that time (which is either rare, predictable, or a harmless visit from Pharos). The Dark Hour, the most important phase of the day for the purposes of the story, is the one phase of the day that is completely ignored and invisible during the course of a normal game day. The feeling that the Dark Hour is insignificant in of itself is only amplified by the fact that, supposedly, normal Shadows almost never leave Tartarus and the heroes must enter Tartarus in order to fight Shadows. This transfers almost all of the focus from the Dark Hour to Tartarus, and what little focus is left on the Dark Hour is taken up by the full moon events, making the full moon seem more dangerous than the Dark Hour. It seems like a waste of the setting's potential, though I admit that it would be hard to make better use of the Dark Hour without completely changing important parts of the game's structure.
One thing the game designers could have done to make better use of the setting would be to create more scenes in which the sudden transition from the normal evening hours to the Dark Hour takes place. Perhaps they could have created a sequence in which the members of SEES are doing some normal event, like hanging out with some friends from school, up until the stroke of midnight, at which point the Dark Hour comes, Transmogrifying everyone but the Persona-users and leaving them alone in the darkened and distorted city. More scenes like that could have even helped make the isolation and hardships of the Persona-users, the people who care forced to see the hidden dark side of the world in a way no one else can, much more clear. Simply having some kind of scene where a Social Link character is visibly Transmogrified or pulled into the Dark Hour and threatened by a Shadow would have helped. After all, since normal people can't remember anything that occurs during the Dark Hour, characters could be pulled into the struggle for a short time without permanently affecting the daytime school stories. Even just having Dark Hour events occur during the Yakushima or Kyoto trips would have been interesting to see.
It really is a shame that the incredibly strong imagery and well-designed concept of the Dark Hour were not used to their fullest in Persona 3. According to what I have seen, Persona 4 will be using a completely different framework, so it looks like the Dark Hour may never get a chance to live up to its full potential as a setting.