There is a lot I could say about the ending to Persona 3, but I am having a lot of trouble narrowing down how to start because it simply has so much good stuff packed into it. I guess I may as well just summarize a few thoughts I have had about it.
1) The set-up for the final battle and ending, including the final climb up Tartarus across January (which builds up the Judgement Social Link and unlocks the ultimate Persona), the last meeting between the SEES members in which they make the pledge to meet again even if they lose their memories, and the last battles against the members of Strega, is nearly flawless. I suppose the entire cult thing was pointless, but other than that the last month, with its severe change in tone and music, was very good.
2) The final battle was really dramatic and well-done. There was nowhere more appropriate for the final battle to take place than the top of Tartarus, and the final battleground set amidst dark clouds beneath the full moon was spectacular. The battle itself, involving the countdown of all of the Arcana used by the Shadows building up towards Nyx Avatar unleashing its true power, was also very dramatic and sufficiently impressive for a final battle.
3) The sudden revival of Nyx Avatar, the revelation of the true, monstrous Nyx within the moon, and the beginning of the end of the world were expected, but still very welcome twists to the game. After all, given all of the discussion over the past few months of the game of how Nyx was invincible, and the importance of the hopelessness of the heroes' battle to the game, the battle shouldn't be won that easily. No videogame with a story based around saving the world should finish before the end of the world is in full swing.
4) It is a cliche story twist that has been parodied time and again, but the whole "in the world's darkest hour, the hero gathers the power from his friends in order to gain new strength" idea is a logical and believable conclusion to the entire Social Link system, so it actually works rather well when it is used here. I like the fact that all of the Social Links that have been maxed out are referenced, I like the resulting, undefined ultimate Persona card (which is certainly The World card even if it is not called such), and most of all I like the fact that the elevator-shaped Velvet Room actually reaches its destination and opens its doors to the light for the first time, as if it is symbolically carrying the hero to his final battle and the conclusion of his story.
5) The scripted battle against the core of Nyx strikes a nice balance between dramatic elaboration and keeping things focused and to the point. I like the fact that the enemy's ultimate attack goes from nearly killing the hero to be completely ineffective against him as the power of his allies surges into him. Also, the fact that the Great Seal move uses up all of the hero's HP is an important detail that properly foreshadows how the game ends.
I was really expecting the ending to conclude shortly after the battle against Nyx, but I was rather pleasantly surprised to see that the ending had only really just started by that point. The hero returns from his battle, the world is saved, and time jumps forward to a month later at the beginning of March, where the parts of the ending I really want to talk about take place.
In a moment of great parallel between the two endings, the next part of the ending starts out exactly the same way as the "Kill Ryoji" ending began, with everyone having lost their memories and continuing on with their lives, speaking about fellow members of SEES as if they were total strangers. However, instead of ending the sequence there and jumping to three days later like it happened in the other ending, here it continues on to the rest of the day that follows, and control is given back to the player as if it were a normal day like any other in the game. This phase is the best part of the whole ending. At this time, the player is free to explore the town, and in doing so can see special scenes for every Social Link at the maximum level that give an epilogue for each story and subplot, as well as scenes involving other members of SEES that show that they have not completely forgotten the bond they share and the things that have changed their lives. It begins just like it did in the "Kill Ryoji" ending, but the freedom that comes afterwards is such a significant divergence from the other ending that it makes it feel like something completely different.
After a few days of being free to see Social Link epilogues, it reaches Graduation Day, the day which both marked the end of the "Kill Ryoji" ending and was decided to be the day in which the characters would meet again even if they lose their memories. Whether it was that promise or just the fact that the SEES Social Link would have maxed out (and thus become unbreakable) twice over between the time Ryoji asks for a decision and the final battle, it is clear that the continuing memory loss would actually be broken in this ending, and when Aigis approaches the hero at the beginning of this day speaking as if the hero's memory has returned (or was never really lost at all), that divergence from the bad ending is confirmed. The final sequence in which Mitsuru slowly gets her memory back in the middle of the same speech she was making in the "Kill Ryoji" ending is almost magical with how effective it is in reversing the tragedy of the heroes' lost memory in the bad ending, but in a odd way that reversal is reflected by another reversal: instead of going out with his friends to sing karaoke, the hero rests his head on Aigis's lap, and slowly closes his eyes...
In a way, there is really no other way that Persona 3 could have ended other than with the hero's death. Much like the idea of the Hero's Journey and the concept of the tarot, the entire story of Persona 3 is essentially a giant metaphor for a person's life. Even more clearly, the hero was bound to Ryoji, an incarnation of Death itself, and was haunted by Thanatos from the very beginning. The hero was given the contract by Death under which he was supposed to assume responsibility for his own actions, and was promised a single year within the game. Because of all of these, I was certainly expecting the hero to die, but I was surprised and impressed at both the fact that the game designers actually went and made it happen, and the way in which it happened. The common, cliche way such things usually happen in stories is that the hero sacrifices himself in the final moment and never returns home, but in this game he does return from his battle with Nyx and lives long enough to enjoy that time and see the happy result of his struggle. Most notably, the way the hero goes is incredibly peaceful and joyful. The hero simply lays his head on Aigis's lap while listening to the sounds of his friends coming to meet him again, and closes his eyes as if for a nap. rather than a tragedy, the hero's death is portrayed as a long-awaited, well-deserved rest. If it were not for a large array of subtle foreshadowing and the oddly sad tone in Aigis's voice as she talks to the hero, it would be impossible to guess that he had even died. Honestly, more than anything else I consider it to be a beautiful ending.