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I didn't like how some things were just a copy paste from XY. Character customization and lack of BF actually bother me the least.
Terrible stubby trainer models and lame battle intros which were also in XY. Many of the trainer models don't even have turning animations and just slide to face you, which is incredibly lazy and awkward to look at.
Delta episode was such a chore and wasn't interesting at all. Ride to space on M Rayquaza was pretty cool but Deoxys can get accidentally OHKO'd by M Rayquaza and you'd have to do all the catching him, battling Zinnia and go through the cutscene again which ruins the mood.
Bosses (Aqua/Magma, E4, Gym Leaders, etc) are also no challenge at all, which is bad because battles feel more memorable and fun when they're at least even just slightly challenging, rather than just sweeping all of their pokemon. The only trainer who gave me just a bit of trouble was Steven, which is good considering he's the final battle.