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To differentiate from XY, from the first visit to Lumiose, you go to Laverre City instead of Camphrier Town, then get your Mega Ring in Anistar (and the postgame upgrade is in Shalour).
Terminus Cave replaces Geosenge as a place you visit early on that later turns out to be important.
The player must be present when Team Flare captures Xerneas and Yveltal. Being there when they get the Poké Balls of all things and then missing the actual encounter with the Legendaries was so underwhelming.
When you loop back to Lumiose, you go to Coumarine City.
This lands you at Geosenge Town with seven badges, at which point the plot picks up dramatically and the player seeks Zygarde in Terminus Cave for help.
Grant is the eighth Gym.
Diantha actually does stuff in the plot now - like Cynthia, she AT LEAST gets updated to appear during the Team Flare climax.
Malva actually does stuff in the plot now as well.
Gym order is now Viola, Clemont and Bonnie (double battle - they're right after you get your Kanto starter - and specializing in Pokémon with Plus and Minus), Valerie, Olympia, Wulfric, Ramos, Korrina, Grant.
New Megas. Gym Leaders now use Megas, at least for rematches but possibly as early as Olympia (right after you get your Mega Ring).
Zygarde Cell hunt now records how many Cells you've found per area instead of overall, so you can keep track more easily (but it doesn't tell you how many there are to find in each area).
Level curve is now balanced to the Experience Share. Assuming the player fights every Trainer, they should never be more than two levels above any opponent.
Like in Generation IV, the Elite Four go up in level as you battle them instead of staying the same (though you can still go out of order), and Diantha is expected to outlevel the player at least a little (two to four levels, please?).
The Elite Four have five Pokémon each. Ramos, Korrina and Grant have four Pokémon each instead of every Gym Leader capping at three.
Postgame: more battle facilities.