Well the anime is just a re telling of her events in the game. not much that's new, I think. Making a separate story mode would be a lot more difficult than the anime.
I wasn't saying it should be a different story, that would be bananas, it would have to be exactly the same, just with some re-recorded instances of gender recognition, most of it would be text based anyway so that's nothing.
In a game like that, when you look at how most RPGs handle gender differentiation in their files, I really don't think it would be too big of an undertaking unless P4 did it in an insanely asinine way.
But since they were willing to shift the story a bit and add a new important character, that to me says it all right there, she would be best served as an alternate protagonist instead of her current role, is my point.
It comes down to me liking Marie in concept but not in execution, so that's why I bought up that, nothing more.