For the the most part I've seen all of the Disney movies that are set to be in KH3, so I'd thank the DVD's and Netflix respectively for allowing me to rewatch all the films, especially At Worlds End as it has been 11 years since I last rewatched the movie.
I wouldn't count on it from the E3 trailer and the Together trailer it seems we're going to do the At Worlds End plot with SDG riding on the raft before falling of the large waterfall into Davy Jones Locker. From there that's when SDG follow the Black Pearl carried by the crabs and meet Jack Sparrow.
I dunno if we will see Beckett, Mercer and the rest of the East Indian Trading company soldiers in the world. Given that the game is now E10+ and the films are PG-13 it wouldn't make sense for SDG to battle them or even show their deaths on screen in a KH game. On top of that it seems that Luxord, the nobodies and the Heartless will take their places instead.
We're not sure what areas we will explore in the world aside from being in Davy Jones Locker, the Maelstrom fight from the films climax and the return of Port Royal. Although I'm interested on how they would end the world following the Maelstrom battle against Davy Jones