Warning contains spoilers for Persona 4
On paper, Persona 4 is everything a sequel should be. It brings gameplay improvements while offering up a new cast of well-rounded characters and a deep, thematically rich story. And yet, it's the fact that it uses Persona 3's gameplay and story as a template really hurt a lot of what this game was trying to do.
Beginning with the plot, the prior game was a dungeon-crawler with calendar-centric timed events and a mix of sim elements. It's a time management game as much as anything else. P4's plot, however, revolves around a series of murder mysteries, but it maintains all the time management elements. It is the single most frustrating part of the game. The story trickles along at the game designers' pacing; despite the constant reminders that victim of the month is under threat. The killer could strike at any time, but on a meta level the player know that they have weeks to mess around. It drains any form of tension out of the events. The gameplay and story are completely divorced. For a mystery plot, players really don't do any investigation. Barring running around talking to everyone about the victim until the game lets you progress. It also takes months for the characters to even consider alternate lines of investigation and speculation rather than focussing on the nature of the victims. One can make excuses that investigative games are a very different beast from a development perspective. And even with a lot of innovation, they still seldom work well. Atlus may have been better off to let players deal with these lesser flaws than be faced with the ones that might arise from introducing more adventure game elements to the series, except Atlus has already made two investigative/RPG hybrids: The Raidoh Kuzunoha sub-series of Devil Summoner. P4 mentions those games and that character by name. Taking a step back, perhaps that sub-series may have been a better match for this plot.
With regards to dramatic tension, the rule for mystery and thriller writing is that as the story comes to a close, the more tense the action and mood should become leading up to the final confrontation with the villain, concluding with a sudden catharsis as all plot threads are resolved. After a final bit of scripted detective work, the heroes confront the killer only to have yet another in-game month to faff about and grind through a tedious dungeon. It's also at this point that the designers introduce a new threat in the form of the evil force that created and controls the shadows in the TV world. The TV world is an element of the game that players have had questions about leading to this point but the characters just seem to accept it without much of a second thought. I'm not saying the malignant forces of the TV can't be an element of the game's conflict, but it should be introduced sooner and resolved when drama is at its highest. Atlus, your pacing is bad and you should feel bad.
The other element of frustration is the characters that the protagonist interacts with as part of the social link system. In Persona 3 most of the social link characters had nothing to do with the story, and it took a lot of meetings and conversations before you got to get to the real meat of each character. It was rewarding when it all worked out even without the level boost and new personae. It also played into P3's concept that being a broader person made you a better monster hunter. In Persona 4 most of the social links are members of the main characters party. A fine idea in theory - the intra-party links in the girl's side of P3 Portable were great additions to the game. In Persona 4, however, all your party members are recruited after having to face their shadow in the TV. In a Jungian sense, players already know exactly what makes them tick; The social links afterward play out as an overly long wrap-up to that conflict, or devolve into just hanging out. Yosuke's move through the stages of grief plays out like the end of Return of the King's extended cut and Chie is so balanced after confronting her shadow that by stage five you have to start helping other kids out with their problems to fill time. Persona 3 had plenty of less that stellar social link characters, but gamers were free to ignore them and find a balance between cool new monsters and cool new story moments. But in P4, social link rank is also tied to combat abilities and persona evolutions. You might not care about Yukiko's waffling over her place in the family business, but want to see her at peak performance come the final boss, well you're just going to have sit through it and smile.
Persona 4 is a wonderful game. It has characters that I love and the video game landscape is made better by it's existence. Unfortunately, there are elements of the game that left me frustrated throughout the entire play experience and I wish it could have been better.