Okay, here's my list:
-Battle Frontier. I would have much more to do in the post game other than catching Legendaries...most of which I have already captured before.
-Friend Safari. I would have loved to seen the Friend Safari return and maybe have a few changes depending on which version you are playing (if in Kalos, my Safari gives you Frogadier, in Hoenn, it would give you Marshtomp). This is a minor thing, though.
-Difficulty settings like in Black 2 and White 2. It would be nice to older players looking for more of a challenge. Again, minor problem.
-Not having the Primals and Mega Rayquaza be so powerful by breaking fundamental rules of Mega Evolution. The fact that Primals don't take up a Mega Slot, yet still have +100 BST on top of good/great abilities, and the fact that Mega 'Quaza just needs a GOOD powerful move to Mega Evolve, freeing up the item slot, is just ridiculous. It makes random battles on the 3DS overly difficult if you are not also using them, even if you have a strong, EV trained team vs untrained Pokémon.
-Not having customization. It is just disappointing to have to go back to seeing the same two character models again after so much variety.
-I would have liked to see Gym Leader rematches. I've missed them as I loved to rebattle them in Platinum and SoulSilver.
-Mega Flygon and Mega Milotic. More so for Flygon as it is one of my favorite Pokémon (not to mention my second favorite Hoenn Pokémon, with Sableye at number 1).
The only things I really cared about was the Frontier, Customization, and the major misstep about the Primals/Mega 'Quaza. The other are just minor complaints.