Hopefully they keep the battle frontier and the Emerald exclusive areas like Mirage Tower and Desert Underpass (maybe as post-game areas, padded out with a few non-Hoenn Pokemon? The likes of Krokorok, Hippowdon, Gabite, Dugtrio, Onix, and Durant could all work well in Desert Underpass. Yamask/Cofagrius is the only Pokemon I can think of right now that would work well in a post-game Mirage Tower. Maybe Golett as well).
I'm also hoping that they keep Liza and Tate's Gym Team from Emerald, since it was challenging as heck! I think it would be cool if they kept Juan as the Sootopolis Gym Leader, too. That way Wallace could return as a post-game champion - so Steven is the initial champion but after you defeat him he retires from his post and Wallace takes over (with Mega Milotic, perhaps?). I think that that could be possible because of some text in RSE, in the message he leaves you in his house where you get his Beldum. Specifically:
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"To <player>… I've decided to do a little soul-searching and train on the road. I don't plan to return home for some time.
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After that he could be battled daily at Meteor Falls with a stronger team.