-No more lunar system. Instead, the game revolves around weather, with foggy nights serving as the encroaching deadline instead of Full Moons. You can check the 7-day forecast on television. It also helps add graphical variety to the town of Inaba, as well as mixing up the daily scheduling.
-Controllable party members, though you can choose AI if you want.
-More Personas (more of a natural progression than 'improvement')
-Male Party members are their Arcanas respective S. Links.
-Leveling an S. Link of a party member improves their performance in battle, though I don't exactly know how.
-You can choose who to spend your lunch breaks with to advance that S. Link (probably just points rather than full level ups)
-S. Links are not necessarily linear; with women, they can branch either into a 'friend' or 'girl-friend' paths.
-Multiple dungeons open up as you advance the story, though I'm still not sure if there is also a game -long one in addition.
-Dungeons are still random, but the engine is less repetitive.
-Dungeons have traps of some kind.
-Dungeons have locked chests that require keys.
-There is a 'Fusion Forecast' system where each day has a different fusion that will give you a bonus (i.e. a special item or stat boost if you create a specific persona, or use a specific persona). The forecast can be checked ahead of time just like the weather.
-Hard mode accessible from the beginning, AND the game is said to be generally harder.
-Alternate S. Links for some Arcana, dependent on which Sports Club and Activity you join.
-You can 'date' at least one guy.
-Wait is replaced with 'Guard', which increases your defense.
-Guarding eliminates your weaknesses.
-Characters will jump in to take damage for the MC, with the frequency is somehow based on S. Link level.
-Hit-all magic that hits one weakness but lands regular hits on others still gives a 'one more'. This sounds analogous to Nocturne's system, so I'm guessing that if you miss the other enemies or hit a null/reflect, you won't get the bonus turn.
-It no longer consumes a turn to recover from getting knocked down. Instead, getting hit with a weakness while you're knocked down can cause the Faint status, which does require a turn to get back up from.
-Shuffle Time also has a timing element introduced, as not only is there there the X-card monty, but also a roulette style shift.
-Questions in story scenes can have an influence on your social stats.
-Mute status ailment that prevents Spells from being cast, but not other Persona usage.
-Enemy reinforcements can show up after you win a fight, like the core SMT games.
-Returning to the first floor of a dungeon no longer completely recovers the party for free.
-The Social Stats are: Knowledge(probably translated as Academics), Bravery (probably Courage), Perseverance (NEW), Communication Ability (probably Charm), Tolerance (NEW).