I don't mean change up the battles, Or even the typical story formula. I love starting with nothing and rising to the top. Some people will say that it's getting old but I say it's like having a Mario game where you don't save Peach. It's just part of the game.
I DO think that battles need to become much faster, 2v2 and 3v3 and rotations need to be more frequent.
It's time for a complete over world and exploration overhaul. More puzzles, new ways to catch and interact with Pokemon, bigger towns and a REAL Online mode, with leader boards, tournaments, matchmaking, etc. The more I think about going through a fully 3D cave in Pokemon the more I wet myself.
I think some overhauls could help improve the games.
Have a hard mode available from the beginning. Pokemon following behind you should become standard. Let's get better graphics in, not totally 3D but something more immersive, i'm not sure sprites need to be the standard anymore. Ideally the 3D from the Pokedex App would be incorporated as the normal battle sprites, offering crisp 3D moving figures.
Change HMs; reducing the need for them is a great start, but perhaps changing them altogether would be good.
Really though, I wish they could incorporate a grand tournament to the game of different classes, copied from Dragon Warrior Monsters. I loved that...