I completed The Answer yesterday, and thus I have finally seen the entire story of Persona 3 FES. It has taken me a surprising amount of time to reach this point, especially considering that Persona 4 is slated to be released in just over a month from now, but it has been well worth it. Persona 3's story has been fun the entire way.
Other than the opening section that introduces Metis and the threat of the Abyss of Time and the final section, the plot of The Answer is built around looking into the various characters' pasts using the doors found at the end of every section of the dungeon. Because of this, even though The Answer is an epilogue to the main game it ends up putting a lot of focus on stories that occurred before those characters became important to the events of the game. As a result, these windows let you see previously hidden parts of the story and unknown character motivations. Many of these, such as the revelation that Junpei's father was an alcoholic and the effect it had upon Junpei, cast a new light on events from the main game, and they all add to the incredible depth and complexity of the Persona 3 cast. However, as much as they add depth to the characters, these scenes don't really do a lot to progress the story of The Answer itself.
One of the most important ideas of The Answer is that the characters are unable to move forward with their lives because they have lingering doubts and regrets concerning the death of the main hero at the end of the main game. In essence, the Answer is a story about grief, the loss of loved ones, and how to deal with that kind of pain. This theme is very powerful in the most important moments of The Answer, and it is brilliantly merged into the game with the constant pursuit of the main hero's shadow throughout the Abyss of Time, but it simply does not play into any of the "scenes of the past" other than Aigis's. As a result, the main theme doesn't show up in the only real plot sequences you see for the majority of the 30 hours or so of gameplay you need to progress through in The Answer. This is really the only significant complain I have about the game's story, and I think the rest is pretty impressive. Well, it gets a bit preachy towards the end, I would have liked to see more elaboration on and reaction to the revelation that Personas are just tamed Shadows (which was similarly understated in the Old Documents of the main game), and the ending is a bit weak compared to the ending of the main game (which was a hard act to follow indeed), but those are minor complaints at best.
One thing that deserves particular praise is the way the complete disintegration of the party and subsequent battle between former allies was handled. This kind of sequence can very easily feel forced or illogical, but here it is surprisingly believable and realistic, given all the complexities of the various characters. The schism in the team is portrayed equally as both a tragic mistake that the characters recognize as such, and a necessity born from the different perspectives the characters cannot reconcile, and is certainly the high point in The Answer's story. Also, the battles against your teammates are a lot of fun and fairly challenging, which helps.
Another thing I really liked was Metis. Beyond being a valuable new ally in the game, she was simply a likable character who played an essential role in the story.
Since this is probably going to be my last post concerning Persona 3 itself, I might as well say that I really liked exploring the Abyss of Time more than Tartarus, mostly because it was less monotonous than Tartarus was. Unlike the blocks of Tartarus that remained uniform throughout, the different sections of the Abyss of Time changed from time to time as you passed through them. Perhaps more importantly, the actual music playing in the background changed from time to time, so you aren't stuck with a single background track for the entire game, like in Tartarus. This helps make the game feel less repetitive, which is a much needed improvement. It probably doesn't go far enough (both dungeons are far too thoroughly built upon a limited number of possible corridors and rooms), but it does help.