Add difficulty modes. Easy mode would be as easy as X and Y are now. In Normal mode, trainers would get better movesets and bosses would get more Pokemon. In Challenge mode, trainers would get even better movesets, their Pokemon would hold items, and you'd get less EXP.
Give Gym Leaders after Korrina more Pokemon, give the Elite Four an extra Pokemon, and give Lysandre a full team.
Do something about the rivals. Instead of them always coming at you together, let them travel separately, flesh out their characters more, give them more Pokemon to train, and allow you to challenge them once a day in the postgame.
Make battle models for all trainers, not just the player and Team Flare.
Change the EV viewing screen to show your Pokemon's EV's in numbers.
Add a way to change your Pokemon's IV's.
Bring in Pokestar Studios, and let Diantha do stuff there.
Make new clothes cheaper.
Move the new Exp Share to much later in the game, like after the 8th Gym. Either that, or just keep the Exp Share as it was.
Allow you to ride your own Pokemon.
Keep the old Pokemon cries as they were.
Give evolutions to weak Pokemon, like Farfetch'd, Dunsparce, Qwilfish, Delibird, Plusle, Minun, Volbeat, Illumise, Luvdisc, Chatot, Basculin, and male Combee. Hell, I'd bring in Basculegion and the Farfetch'd evo from the Space World beta.
Speaking of beta Pokemon, maybe add more of them into this generation.
Make Carbink evolve into Diancie, make Diancie learn Power Gem, and make Diamond Storm a special move.
Add the Venonat line, the Misdreavus line, the Phanpy line, the Shroomish line, the Glameow line, and the Joltik line to the Kalos dex.
Remove the Patrat line, the Trubbish line, the Snubbull line, the Woobat line, the Goldeen line, the Foongus line, the Nosepass line, the Wynaut line, Stunfisk, Cryogonal, Articuno, Zapdos, Moltres, Mewtwo, and Annoying Stupid Flying Squirrel from the Kalos dex. If I have to make them available, restrict them to the postgame.
Get rid of Mega Garchomp, Mega Tyranitar, Mega Scizor, and Mega Charizard Y. Instead, make Mega Charizard X the only Mega Charizard, and give Mega Evolutions to Pokemon like Butterfree, Raichu, Mightyena, and Flygon.
Rework the Battle Maison so that the AI doesn't cheat. Also, add more battle facilities and make a Battle Frontier.
And finally, make Pokemon Z, with a postgame story about Zygarde and one about AZ and his Floette.