Something about the plot has to change, because gen 6 mechanics have destroyed the original story.
Drizzle and Drought no longer bring permanent weather, so how will Magma and Aqua achieve their goals? I believe this has something to do with the "new formes" (which I'm certain are Megas, but that's another topic altogether) we see on the boxart.
As to whether or not the story will focus more on RS or E: the games will certainly have Emerald aspects, no doubt about it. But I'm sure they will retain the major plot elements of RS. I know a lot of people love Emerald, but to me it was very clever to have a team that wasn't evil. Up until RS, only Lance tried to help you stop the evil team. But in gen 3, someone had the common sense to say "wow, this group is pretty evil. How about I gather some people to try and put a stop to them?" In gen 4, Cynthia goes back to being the only person who helps you (granted, that could be in part due to Galactic's strategic use of lame outfits to make people think they weren't threatening), and it was only until gen 5 that we really saw characters besides the player take a stand against the villainous team again.
As great as Emerald is for introducing the Battle Frontier and having Match Call, I'll always prefer RS's plot since it really takes advantage of version differences and makes it known that there are actually people out there who are willing to risk themselves trying to stop an evil organization, not just a 10-11 year old child. I would honestly be very disappointed if these remakes do not have obvious version differences the way the original RS did, and instead took a DP approach to the story.