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If this is more than the Pokedex habitat function from FRLG and BW2, I wonder if it'll mean the game itself, story wise, will not allow you past certain points until objectives are completed.
I mean, they already do this to block specific routes, but it may work different this time and the "coastal" part may be completely inaccessible until a number of badges are achieved, or if the "mountain" region may be blocked until the coastal region is beaten.
Perhaps the main story of the game (most of the evil team plot and the entirety of the 8 badges) takes place in the Central area (where only certain pokemon live, but enough so that there's a nice range but not the entirety of the new pokemon), the remainder of the evil team plot and the Elite 4/"victory road" is the whole of the Coastal region (with previously inaccessible pokemon), and finally the Mountain region will be the Battle Tower/Battle Frontier/thatisalndfromDPPTIcan'trememberthenameof, basically just the main calling of the post game, with old pokemon and the few remaining new ones.
If my last idea is true, and we get more with trainer customization than just skin and hair color, perhaps the MCs will change outfits, or be given different changes of clothes to traverse the different areas - normal clothes for Central, Summer/beach clothes for Coastal, and maybe more rugged clothing for Mountain.