Like the other remakes, hardly any changes would be made to the main story. It would still be the same Story as Ruby and Sapphire. They'd just throw in a small change to some of the cities, maybe add in a few extra traps to the gyms if they don't change the Gym Layout.
A few teams may be redone. And there is the after E4 extra story/Features (Like FR/LG's Sevii Island thing since unlike Gold/Silver, Ruby and Sapphire didn't have an after story.)
Any changes to the story would be small or to give small characters a larger part in the story (Kimono Girls in HG/SS and Bill in FR/LG)
How you get Items would prolly change as well, as a few story items were recieved differently in the Remakes than the originals.
Either way, the games will just be visually updated versions of Ruby and Sapphire. That's pretty much all remakes are.
Hopefully this time though, they use them as 'updated' versions other than just graphics. I don't mean changing the story drastically though, I mean partly to give them better reasons for why they do what they are doing. They were a bit...'lacking of the smarts' when it came to why they wanted to expand the sea/land. It's understandable to want to change the world, but their reasons could use a bit more depth and meaning, if you get what I mean.
I also hope we get to see more of characters like Lanette, etc. It would also be nice to see our mom, etc. make more appearances throughout the region...it would be nice to see it being a coincidence that she decided to visit Norman(dad) around the time of our arrival back at Petalburg for the battle(in that she would be watching and comment afterward).
I wonder which characters other than her and Wally will be popping up more. Obviously our rival will probably play a little bigger role as well(with a fully grown team at the end).