1. Twilight's not going to be a villain unless there some kind of possession or something.
2. Although we see she has very bad 'issues' with being late or her time table changing, this alone won't make her a villain.
3. This would be very dark and the show is intended for children.
It is not likely this will be a future plot. Also why the hating? I dislike Twilight personally but she is a good character.