The game suffered incredibly from a lack of post-game activity. Bad enough that it only provided the Battle Maison, which is pathetic compared with Gen IV's Battle Frontier and Gen V's Pokemon World Tournament.
The game even lacked a side-activity to battling! Gen IV had the Super Contests for the Sinnoh games (which were very disappointing as they were downgraded versions of Gen III's contests) and HeartGold/SoulSilver had the Pokeathlon, one of the best side activities seen to date. Gen V went downhill with the Musicals, but BW2 sort of saved it with the Pokestar Studios.
TL;DR:
More battle facilities.
Needs side activities from battles.
Bring back Pokeathlon!
The Battle Maison is essentially a souped down version of the Battle Tower.
XY would have been great if it had richer post-game content. The Looker side quest was IMO, repetitive and terribly boring. It was a nice add-on to a city (I mean, Lumiose is HUGE, there has definitely got to be crime) and at least we get to know Looker a little bit better but... seeing him for 3 generations in a row is kinda making me sick. It's about the same as me getting sick of Kanto. (Sorry to anyone who felt offended, I didn't start with RBY)
They could have added unique clothes in different regions, and allowed us to download them over GLink/Spot/StreetPass.
Rematches with gym leaders and the E4 should be added. XY was generally a very easy game (made worse with the new EXP share), so true rematches - NOT chateau fights - should be implemented.
One problem which is kinda bugging me is the fact that in XY, there's a considerable lag time between the animation of move sets and pokemon receiving damage for certain moves. Take a look at Draco Meteor for instance, after being hit by Meteors, the Pokemon still stands there as though nothing has happened. Only after the Meteors have disappeared then it takes damage. I hope they'll fix it in the upcoming ORAS, needless to say the X2Y2/Z version.
However, I can definitely see Game Freak make a Pokemon Z. I cannot exactly think of a possible sequel given XY's storyline, but they could certainly fix all these problems and enhance the storyline with a Z version.