How I see it, they could start with the normal Safari Zone that was in the originals. Then, for the post-game there are one of two things they could do:
1. Use the Emerald expansion that adds Pokémon that weren't included in the Hoenn Dex originally.
2. Do something like with Object Arrangement in HGSS where you can place objects and it'll influence the Pokémon that appear. That was a neat arrangement and a cool part of HGSS' post-game, even if it was time-consuming it was still something nice.
Or they could make it so the Pokémon change daily like with Sinnoh's Great Marsh. Just a few ideas as to what they might do.