I'm really hopping they do implement it, but I'm sure they will. I'm thinking it wont really effect the story too much; It'll probably take effect after the main story anyway.
I'm hopping rebattling them is straightforward though, unlike HG/SS.
I think it would be cool if, after the main story ends, you rechallenged them by finding them out in the different routes throughout the game, at any time, not just talking to them in their gym at a certen time to get their phone number. Like the water dude could be found out on an island or by the beach or something.