You basically just described the entirety of Inazuma Eleven 2: Firestorm and Blizzard in a nutshell (Especially in the case of Fubuki/Shawn Froste. For a game of its type, it gets pretty deep when compared to the game's subject matter, and I definitely recommend it (one of my favorite DS games). Even though the game is about Soccer (though you don't have to be a sports fan to enjoy it, I don't even like soccer in real life), the way they go about building the conflict not just in Fubuki but in other characters is rather clever, and the game itself is great, and this game is easily the most appropriate for what you have in mind (and for what I have in mind currently).
Persona 4 is this as well, and it's also one of my favorite games period. It does this on more human level than most other games you'll find, as well as probably a more compelling one. Of all of the games that follow the criteria you set, I certainly recommend this one the most.
The World Ends With You may also qualify, though its conflict is less out in the open and more something that comes into the light slowly throughout the game and in the postgame, but it's still an excellent title that's definitely worth checking out.
Then, of course, there's Final Fantasy IV featuring Cecil, though this conflict mostly exists in the beginning. Regardless, the game has a great story and, if you like Turn Based RPGs, you'll like this one.
