While I wouldn't be too bothered if it didn't happen, I feel like bringing back the female protag option from the PSP version of P3 would be neat.
Aside from that, I feel as though battling some out-of-control god is overdone at this point. P3 did it, P4 did it, and P5 did it. So I think it would be really cool if they diverged from that, and had the end-antagonist of P6 not be some divine god, and maybe not even a demon from the depths of hell, either. Maybe just some guy, or gal, who might have the ability to wield Personas like you can, but instead choosing to use them for anything but the right reasons.