The reasons Persona 3 is a great game, while most other JRPGS are merely medicore games with the occasional disctinction of great storytelling, are numerous - but there is one key gameplay distinction that sets it apart from the pack - its startling lack of grinding.
Almost all other JRPGs are fairly trivial. Their experience based design makes skill no object; the only obstacle that stands between the player and ultimate victory is the player's time. There are no interesting decisions to make outside of combat, and the combat itself is trivial. When the player loses a battle all he has to do is go back to his last save and grind his heart out. It's not hard, it's just time consuming. In fact, there are certain JRPGs where one can breeze through the rest of the game by leaving the console on one night and taping down the X button (and come back in the morning level ninety-nine).
However, Persona 3 has managed to create a system where mindless grinding is not only ineffective, but impossible. To explain this system, one must first understand the details of the game. Persona 3 is broken up into days, and each day is broken up into several periods of time (e.g. late night, afternoon, early morning). Occasionally, you will have choices during the early hours of the day, but most important gameplay choices fall into two periods of time: After School and Evening.
In Japan, they have school on Saturdays. Who knew?
All the non-combat related choices you make during these times fall into three categories: choosing to improve your character's social skills, choosing to strengthen your character's relationship with another character, or choosing to enter the dungeon (the only way to fight). Now, you can go to the dungeon every night and grind on low level floors; however, you won't get very far. First, your characters grow tired quickly in the dungeon, and start to deal less damage and take more of it, rendering your party ineffective. Second, the rate at which your party tires is independent of the strength of the enemies you're fighting - that is, they'll be just as tired after a hundred boss fights as they will be after a hundred regular fights. Since harder enemies give more experience, grinding will leave you with exhausted, low level characters, while progressing in the dungeon will allow you to fight harder enemies and at least you'll end up with exhausted, higher level characters.
However, going to the dungeon every night in and of itself is inefficient. It's much better to hit the town and sing some kareoke when you're tired, as it's less exhausting. Improving your social skills (by singing, apparently) will help you find more social links, and choosing to strengthen those social links will allow you to summon stronger persona of a certain type (persona are a physical extension of one's psyche, the game explains).
Thus, one who goes to the dungeon every night will end up with inefficent, high level characters with weak personas, and one who goes out every night will end up with many weak personas (as they will have many social links) and weak characters. Similarily, one who chooses to have one or two very strong social links will find themselves with a few strong personas but a crippling lack of flexibility. In addition, Persona 3 makes you battle bosses every month or so, regardless of the actions you take, forcing you to weigh long term profitability (social links which will help you throughout the game) against short term profit (dungeon crawling for quick cash before the next boss). The key is to balance these activities, which is no easy task, and it is here that Persona 3 finds a sweet spot of game design - in decisions that most other JRPGS brush off as trvialities.
