DISCLAIMER: These ideas are my own. If you share the same or similar ideas, than you can post regardless. But please spoiler tag it.
I'll update my list when the game officially releases.
Spoiler Show-Not letting us at least explore Radiant Garden's castle with Leon as the party member (and maybe Rinoa in the credits).
-Not letting us explore the Old Mansion.
-Not having Unversed be the main enemies of Arendelle.
-Not having Dream Eaters be the main enemies of Toy Box.
-Not having Neku in San Fransokyo as a second party member (he doesn't have to be native to it) or making the Reapers the antagonists.
-Not having Princess and the Frog as a world (Dream Eaters could be the enemies here, too).
-Not having Ignis introduce us to the bistro (and Remy, by extension).
-Making the 100 Acre Wood Keyblade transformation a Shooting Star clone when they could've easily made it something like a giant hunny pot.
-Not having Faris (FF5) or Balthier be part of the Caribbean.
-Not letting Riku have a playable section in Arendelle (he and Sora could take turns throughout the world).
-Not having Aqua be a minor antagonist in San Fransokyo.
-Not putting in a fight between Aqua and Sora in Castle Oblivion.
-Making Ralph the only Link character Sora hasn't met (or mostly just reducing Link summons to people Sora's met).
-Ditching the Coliseum cups.
-Not giving Lea a new outfit.
-Donald and Goofy aren't stuffed animals in Toy Box.
-SDG don't get superhero outfits in San Fransokyo.
-There's probably no toggle button for the wall-run lines (I didn't mind them at first, but now they're just CRAWLING IN MY SKIN)
I'll update my list when the game officially releases.