Following the trend set by previous remakes, ORAS will probably draw a lot of its plot from Emerald, and involve Rayquaza during the legendary encounter towards the end of the game. They'll probably bring back the stress on weather from RSE, what with Team Magma and Aqua being so infatuated with drastically changing it and the legendary trio being based of it. Nothing much will change, per say, but rather lengthened and expanded on.
The trend from the previous remakes (really this only touches HG/SS), the third version's story wasn't even a major point. You get to the point that was mandatory and then you get a few forced encounters along the way, but half way through, that's pretty much it and you have to wait until Post game to continue it.
If that is how this goes, then the events of Emerald won't be in effect as Emerald had the exact same story as Ruby and Sapphire with the only exception were the alternating of which team you were fighting against at what points. Since there are two games, they don't have to follow a path that was made because there was only one game.
If anything we're getting the same story that we had for Ruby and Sapphire. Magma are the big bads after Groudon and Aqua opposes them on the sidelines while you do the major work. Groudon awakens, starts to heat things up. Here is where it can alternate, you can beat Groudon and it retreats to which you can follow it then and there and fight against its alternate form, or alternate idea, you fight it again later after it becomes stronger (like Kyurem in B2W2) and is in its alternate form. Same thing for Sapphire. Aqua bad, Kyogre flood. Rinse repeat.
Could pull a Emerald later on, where opposite team awakens their big bad beast and they do the iconic fight to the death where you can awakens Rayquaza and stop the fight. But then something happens and Alternate form mascot appears.
Based on the CGI from the preview, it stands to reason, we may have the same direct stories in a sense. We know there will be minor edits to the main story just to try and keep it fresh, like all the encounters with the opposite gendered character in HG/SS and all its awkwardness. They are more than likely to be pulling from the originals more than pulling from Emerald in the sense of the main story where we'll only focus on one bad team.