If they do happen to keep them version exclusive, then what will they do with either the Whirl Islands and/or the Tin Towers? I mean face it, there will be really no point visiting these places without the legendaries. Now, if they held the storyline centering the Legendaries like what was done with RSE and DPPt, then I get that. Except, Team Rocket was never after them, but rather to gain extra money, and fast by doing crime around Johto.
Seeing as this is so, there would be no point in keeping them seperate. The purpose for the two versions is to hold exclusive Pokémon, and for this it means something other than the legendaries [I would think.] Anyway, if they happen to do seperate them, unlike how it was done in the orignals, then they'll definitely need to make an improvement to two certain locations to actually give the place a point to be apart of the game.
They definitely cannot remove [Tin Towers/Whirl Islands] them depending on what version you have, because that'll jstt create an overdose for complaints. It'll definitely be a bigger issue than what the new female had brought for some time. To me though, nothing should be altered with these two, as it made Gold and Silver different as well as it'll make HeartGold and SoulSilver different too.