Let me make this clear, Persona 3 is the single most brilliantly designed game I have ever played. The only games that I could even be convinced to dethrone it with, are the other Shin Megami Tensei games, since I haven't had the pleasure of playing them yet. Before I go on though, note the word I used, brilliant. I didn't say it was the most original, most novel, most beautiful, most popular, etc...
It's brilliant in it's subtlety, and the seemingly effortless grace with which it destroys the biggest problems in game design. By and large, games have the subtlety of a fireworks show followed by a Slayer concert. Loud, obnoxious, in your face, are practically watch words of the entire industry from top to bottom. Time is always measured in milliseconds (literally in many modding tool sets), story is an excuse of varying thinness to shoot/stab something, and choices are generally some amalgam of "our way or your fucked" and "I choose the blue door... both of them". Persona on the other hand is quiet, confidant, and capable.
There has been a constant argument as to how story and game play should interact. Generally the Eastern ideal is strict separation, while the Western ideal is to take personal realistic control of the story. One is generally too light for the palette, the other faces the problem that most fictional heroes are actually pants on head retarded/crazy and nobody would ever do the things they do especially if it is just a game. Persona approaches the problem by having a strictly defined set of rules in the game section, then begins to tie in your performance to choices made in the story section. Even better, if you choose to get involved in the side stories, it gives you a means to circumvent the rules in the game section. According to the rules of persona fusion, you cannot fuse together a persona of a higher level than your character's those are the rules. However by exploring the stories of minor side characters you form social links. These links give a persona of their archetype a huge experience bonus when fused, allowing the persona to level up, beyond the level of the main character.
This is hugely effected by the property of choice since you have to choose which friends to form and support those links with. Persona takes a diametrically opposed view to the Western ideals of choice, i.e. where the player is given the impression they can change the direction of the story, but have no options in how they experience the story. In Persona, the main storyline will advance as written, without deviation from the script, but you choose how you will experience it and in many ways who your character really is. You have some dialogue options, but more importantly, you will decide how you approach the game, where, and with whom you spend your time in-game.
I'll come back to choice in a moment, but first I need to talk about time. Playing Persona beginning to end takes a pretty damn long time, but that isn't even what makes it so important. In Persona, time flows in a relatively fluid fashion. playtime is packaged into days and sub packaged into times of day, most days are school days as well taking up the morning and afternoon in most cases. After school however, you have the chance to decide on a variety of destinations and characters to spend your time with, but this takes up a certain package of time. I'm not going to go into the various activities and exactly how they overlap or interact, but suffice it to say you can't do all things in one day. Not only that, but you can't do all things, or meet all people on all days. Learning how to manage your time between the dungeon crawling segments, the story segments, your school performance and getting to know the side characters you particularly care about is actually a daunting task at times. And even more than that, your time is quite literally limited, you only have about a year of in-game time to do whatever it is your going to do. The game also doesn't seem to imply that it's going to give you a freebie and let you suddenly win if you failed to prepare in all that time, each monthly encounter being a significant enough step up in strength to remind you that you probably could have been training more.
And there in lies the real choices the game presents. While you can't stop the game from moving to it's inexorable conclusion, you can choose how well well you "live" up to that point. The addition of status ailments that can utterly destroy your ability to play the dungeon crawl well and prevent you from exploring the story as you wish for failing to get sleep also means you can't just cut rest from the schedule to make it all fit. So every in-game day you face a wide array of choices that you know will effect your experience not only now but also far into the future across any number of individual play sessions.
Also there is a certain elegant balance to the system. Unlike many games where there is no appreciable penalty for gaming the system, in Persona you have to literally force yourself to cut out well written segments of side story in order to min/max your "build's" social links. Even more so, once skipped a player can't experience content again without starting from the beginning or some similar save point, meaning they can't actively choose to min/max their character and experience all the content at the same time, it's one or the other. This ties back into choice, since every choice comes with a reward, but every choice also comes with a penalty. It's perfectly normal to make a choice in Persona and wonder if an alternative choice might have been a wiser use of your time, and it's also perfectly normal to be happy you made the choice you did, because otherwise you might have missed out on what you just experienced.
Final word, brilliant in the way that a great work of art is. It'll be held up as an example of greatness long after myself and everyone reading this is six feet under. Though it's hit or miss whether it will ever be "main stream".
P.S. This is not a review in the usual sense. I'm not trying to inform a consumer as to whether or not they should go out and buy the game. The purpose is to point out great game design, so that other designers can learn from the brilliance I see in their work.