I definitely believe Mr. Briney and Peeko will make a return; however, I can't see them having a bigger role. After all, after you get Surf he isn't really needed until post-game, where he then runs the S.S. Tidal, allowing you to travel to the Battle Frontier as well as have a few more people to battle when going to either Slateport or Lilycove.
That being said, if they make the Southern Island accessible I can definitely see him taking you there. It's also possible that if they decide to add more islands (like Kanto) or even allow travel to another region (doubt it, though) then he'll be the one to take you to those places. But that's all his role is: a captain who takes you to places by boat.