They could still have both teams involved, just give one a bigger role depending on the game(Ruby- Magma bigger, Sapphire- Aqua bigger).
Maybe you could foil one team(the lesser one in your game)'s efforts at reawakening their pokemon, buying the other team(main one in your version) time to get through with their final plan(s). This way we would still get the extreme drought or rainfall, etc...
Except there's a problem with that. Where would Rayquaza fit in(due to it being used to calm down the fight of both)? It would seem pretty stupid to awaken it just to calm down one, imo, as the colossal battle between Groudon and Kyogre added much more to the depth of the story. It would also be a waste to just leave it waiting until after the E4, with no interaction in the main plot, throwing away Emerald almost completely. Even the Battle Frontier wouldn't do it as much justice as being able to add in the main 'Emerald' element, if you get what I mean(pretty much is the combination of the two).
I say this because I highly doubt they'd choose to just make one version over two, but then again this time they have a bit more on their hands: They probably would want to make them true to the originals, but without scrapping Emerald completely.
That's why I would see them making two different versions like they have, but just make one team more dominant than the other, depending on which version you choose to get, although I'm not sure how they'd implement the Rayquaza storyline then, if one gets defeated and the other succeeding(which is all I can think of atm that would give them a separate feel, hm...).
This is a really interesting thing to think about if you think about it...