1) More endings.
At the end of the game, it barely feels like your choices mattered outside of the most super-important conversations. Plus it gives great replay value. Catherine is a great example so I know Atlus can do it well.
2) If you aren't adding gay options, stop it with the 'older women' romances, please.
Atlus looks like a hypocrite when they aren't willing to add gay options but sleeping with your teacher and your doctor while in high school is A-OK.
3) Player customization out-of-dungeon
Even if it was just putting on different outfits or trinkets. People always love this.
4) Bring back from P2/P1 party members being able to have different personas in battle than the one they start with
Even if it was limited like they could only use personas of their arcana (like Ann can only use lovers arcana personas) or personas that didn't 'suit them' were weakened/could disobey/cost more SP/etc... This would make every party member more useful.
5) Your equipped Persona can cause things to happen out-of dungeon (like new dialogue options).
Like if you have Mara as your equipped, in conversations you can say really out-of-line pervy things that aren't available otherwise or just arcana based things like having a hermit persona equipped during exams gets you better marks.
