Help her set up her character in Mass Effect and get her through a bit of the game initially and I'm pretty sure she will become invested in her character enough to really get into the game. Especially if she likes morality based games she going to have a lot of fun choosing her personality and having consequences for her actions.
Other than that for jrpgs I would recommend Lost Odyssey and Golden Sun. Lost Odyssey because I think she might enjoy the story and Golden Sun because you said she liked pokemon so I think the play style would be to her liking.
Maybe you could even try Crackdown too seeing as how its pretty cheap now. She doesn't like fps games or shooters right?
The definitive evidence that video games turn people into mass murderers
