Regarding Jirachi: I predict that they will find out that the thousand-year rule for Jirachi is due to something that happened a long time ago and the gang will eventually find a way to free him of the 'curse'.
I also predict that when this happens, or something similar to it, the 'true evil' will show itself and the main characters will have to fight it in an epic battle, using ALL of the Legendary Pokemon. This is, of course, after it destroys 90 percent of the world. Still, they gotta give it their all to save the last 10 percent...
Max will of course end up with Jirachi in this case, but it will be after he becomes a Pokemon Trainer (Gym Leader??).