Some ideas:
Vastly expand the Hoenn Contest system for compatibility with Amie + reduce the randomness and players' general inability to influence the outcome of matches; really, contests could be decided really early on, yet it takes a quarter of an hour to then finish the damn things.
Condense or shorten the water routes between Ever Grande and Pacifidlog, compensating for space by adding more (excuse me) depth to the diving portions. Mirage Island should earn some extra too, perhaps Latios/Latias/maybe Deoxys/whatever.
Add PWT features to the Battle Frontier, pls.
Designate a rival (either Wally or gender opposite) and friends a la X/Y; if possible, give Prof. Birch some actual involvement with the main game following early-game.
No Game Corner anymore, so something will have to replace the one in Mauvillea new mini-game, maybe?
Streamline biking system, either by using skates for Acro-accessible areas and adding gearshift to regular bike or by making it a multi-purpose mountain bike.
&c.