P4 is a game with a high amount of potential which it doesn't achieve due to a lack of character development and a somewhat flawed moral on why you shouldn't lie to yourself.
I was excited to obtain new characters the first time playing as I was eager to see how they would work on dealing with their own issues. How disappointed I was when I learned that the characters don't develop AT ALL. Whether or not you spend time on their S-links, nothing really changes about them outside of battle. By the end of the game, they're still the same person, which brings me to the anvilicious moral of the game...
The game makes it obviously clear that you shouldn't lie to yourself and that you should accept who you are. A commendable effort... HOWEVER, this moral takes a rather unpleasant light once you reach the 7th storyline boss. Simply put, I felt that the moral of the game shouldn't have been "Don't lie to yourself" but rather "Make yourself a better person." Just imagine if you-know-who were to accept who he was and how much more powerful the game would've been. Which leads me to Yosuke...
I can't believe that the writers at Atlus took such a huge step backwards from Persona 3's Junpei. It seemed rather simple: Both are class clowns who suffer similar tragedies and they both share the same arcana. While Junpei becomes more mature because of it, Yosuke unfortunately acts like an obnoxious imbecile who disrespects his own teammates, failing to realize that his behavior throughout the entire game might've been the reason girl he loved didn't love him back, making it hard for us to disagree with her when she said that "he was a real pain in the ass".
The S-links are also another issue I have. Other then Nanako, Dojima, Naoki and Naoto, all the other S-links were bland. While the Arcana/Ally bonuses are quite helpful, it does nothing to affect the main story which feels rather wasted seeing how much it would've worked with the moral I mentioned above.
As for the main mystery plot, I only had minor issues with it (talking to civilians...) though one scene near the end of the game was quite the head banger (before unlocking the 7th dungeon). What happened afterward should've been avoided.
In short, P4 is a huge disappointment in terms of story. Hopefully Persona 5 will fix these issues as P4 truly could be something amazing.