What I would like...
1.) Multiplatform: 360 needs more love too!
2.) More elements: After playing alot of SMT games lately, I do get tired of seeing Bufu, Agi, Mudo,Zio, etc spells.
3.) More Interactivity: I KNOW this won't happen, since Atlus is a small company. But it be cool seeing your Social Links walking around doing their own daily task, like it GTA 4. They could call you to hang out, or be surprised when they meet you.
4.) Bigger overworld: Seriously, if your going to make us stay in a town for close to 80 hours, the best you could do is make it bigger! Probably not GTA4 level, but lots of Shops and entertainment stores could be cool.
5.) Being able to dress your protagonist: hell, they could make it a game play element! Probably you can't go to someones party without wearing a tusk.
6.) Experimenting with Real Time Combat: Probably a bit controversial, but I'd think it would have a more mainstream appeal if the combat took place in realtime. Kind of like...no, exactly like Devil Summoner 2's combat system. How cool will it be deliver rapid blows, backstepping to dodge and attack, and delivering an Agidyne spell as a finishing blow?
7.) Make test be on stuff you actually learn in class, rather than random facts.
8.) More persona users. Takaya and Jin's battles were pure epicness!
9.) Get rid of the Kun, Chan, Sempai, etc, and to compensate put a Japanese language track. Too me it just sounds awkward.
10.) More animations for Personas
11.) Less recycled shadows ( Persona 3 being the main offender!)
12.) More animations for party members.
13.) Optional party members: Wuldn't it be cool if your part really consisted of the people you decided to form social links with? This could also change up the plot of the story.
14.)Maybe a few minigames: Like a dancing minigame, racing minigame ( For like track sports event), etc.
15.) Alternate weapons for party members.