OK. I have decided. Since there are tons of people remixing Xenogears all the time, I have chosen to do a game that has never been covered here. Nobody will ever guess who my villain is. I don't need to worry about anyone taking this one, so I won't even try to claim it until I have a WIP for it.
Hints:
Female, PS3 RPG, not a final boss, can be fought three times. Let's see if anyone can guess before I submit a WIP, which I expect will be this weekend.
EDIT: You fight her four times, not three. Here's another hint: Her name is an Italian word.