Personally, they should just add Stadium/Colliseum's features into the post-game of mainline pokemon games, the mini-games, the tourneys, the 100 trainers endurance could make a comeback, etc. Oh and since pokemon is 3D, make the pokemon battles feel dynamic, and by dynamic i mean...
-Weather effects that reflect what happens on the field like Rain droplets actually fall on pokemon and in some cases, pokemon start looking wet. Some pokemons could have some reactions to some weather like wiping their sweat when they're under the sun after X turns.
-Pokemons having actual reactions to what they're getting hit with and what is going on currently on the battle like; if they land on spikes, they show they're hurt by spikes or stealth rock or whatever. And their idle animation looks different depending on their lifebars or status (poisoned 'mons start to look ill, for example). While also giving pokemons more idle animations or something, i don't like how some pokemons just have the same neutral stance, it could also depend on nature like a Brave nature pokemon's idle stance could look like he's taunting or eager to fight.
-They could also bring back following pokemon as a silly way to expand pokemon amie, something like a minigame where you play hide n seek with your lead pokemon and search it in a city/route you're currently in (if city, you can find it in a trash can or hiding somewhere, if route, you can encounter like a normal pokemon). And maybe in the case they bring back lead pokemon following you, it could react to whatever that happens in the story. Because let's face it, expect the next pokemon to have cutscenes.
But this is just all my opinion, i just feel like Pokemon as a whole should be more dynamic and interactive.
