hi, it's me, the person who found this thread on google and made an account just to post in it.
This game has been bugging me for a really long time. It was a PS1 RPG (it could possibly be PS2 tho). I think it was all 2D, and the main sections were isometric. There were two playable characters that you switched between at certain points in the story - one was a hero and the other was a villain, and i believe the villain wasn't human. But, like, "not human" in the way that laharl isn't human, the anime demon/monster type of guy. Don't quote me on this, but I think he was going to school to learn how to be a good bad guy? In any case, you would swap between the two of these characters, and their stories converged at one point where you play as the hero and you fight the other character as a boss, and he joins your party when you defeat him.
I don't really remember anything about the overarching story to the game. It had an aesthetic similar to Final Fantasy 9, but I know it wasn't that.
Games I know aren't it: any Arc the Lad, any Final Fantasy, Chrono Cross, Breath of Fire 4, Threads of Fate, any Wild ARMs, Disgaea.
These are all games that I've played and know aren't it, or have been suggested by friends and I don't recognize or haven't played. I could be wrong though... If it is one of these I'll hate myself forever.
I'm half convinced by this point that it doesn't exist, and that I dreamed it up, or maybe it's some weird memory amalgamation of several forgotten games that are getting more and more jumbled up as time goes on. If anyone can tell me this game, I will pledge myself to serve thee until the end of days.