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Can't it be a combination of the two? What about Heart Gold/Soul Silver? Wasn't that a type of remake? A sequel would be more interesting, but they could still make changes and improvements if they decided to just do a remake.
Unlike bw2 i don't see any point to a sequel, Maxie and Archie both realized what they were doing was wrong and won't be a villainous team anymore. Having a new team come and takeover would be boring as well. i'd say a prequel that explains why Maxie and Archie were so adamant about their goal maybe a catastrophe that'd eliminate the gen 4-6 pokemon from the region.
Sequel based on one of the other legendaries, maybe Deoxys with the 8th Gym leaders being the twins, but grown up. Bring the extra islands into the main story, have Fortree even higher up, expand what Dive can do. Unlockable Emerald version played on the PC with the current Gen's battle system, beating the Emerald copy lets you import those pokemon into your main game or something.