This was what I meant. HG/SS had pretty much the same story, except they added a little more importance to Lugia and Ho-oh in them. But still, same story, and even Crystal had the basic same story, but Suicune was much more involved. But because those games all had very similar stories, Suicune's part in HG/SS didn't take away from the original games. Using Emerald's story in Ruby/Sapphire remakes would change them, and is something that Game Freak wouldn't want to do and fans wouldn't want to see it happen.
This is why I said that if they were to use Emerald's story they would be better off remaking one version based on Emerald. There's no point in remaking Ruby and Sapphire if the basic stories are going to change. There's no way to mix these stories to make sense and stay true the originals either. Scrapping the Rayquaza story sounds much better than having both games basically use the Emerald storyline.
That cutscene wasn't in Ruby or Sapphire, so Ruby and Sapphire remakes wouldn't need it. They could easily make cutscenes for Groudon and Kyogre to show their influence in the weather, just like in HG/SS where they animated the entrances of Lugia and Ho-oh and in B/W where they animated Reshiram and Zekrom.
This is another reason why I think we might possibly not get remakes at all. Some people want the games to be the same, while others want Emerald's story added (which makes no sense if these are to be RUBY and SAPPHIRE remakes). Regardless of what they do, Game Freak will receive backlash. It might be a better idea to just leave the games alone and not remake them.
That point about GF being backlashed isn't a reason to not make them either then; they are
still going to get some crazy people who have been waiting forever and ever with the many 'hints' to flip out.(not saying they should 100% be seen as such, but you get my point).
Just because HGSS had less differences of the originals to deal with does not mean they would be forced to make the remakes 100% like the originals as that would mean nothing new at all would happen. Mixing new and old is what gives both veterans and new players something they can have fun with, and in this case it would also include throwing in Emerald elements so as to make them feel more...complete.
What was one of the main things separating Ruby and Sapphire again? Each's main team being more 'dominant' than the opposing game's main team. Does that mean the other team
did not show up in the opposing game at all? Heck no. We still saw them, except on the more innocent side of things.
Imo, this is where they can keep the main idea intact, yet also add in some Emerald to it.
They can make us face the main team noticeably more than the opposite game's team(they could get the 'lesser' plans), but we could also get caught up in a little of their schemes as well. After facing a bit of each team, we realize we aren't able to keep up with both sides, so we decide to persue the more threatening team(the version's team you picked, one with bigger schemes). Being caught up with both teams for a bit, we get a little behind the main team and in the end they are able to wake their ancient. The opposing team, no longer being chased by us, are somehow able to awaken theirs as well.
Ya di da...the battle in Sootopolis. We get Rayquaza to calm them down. Ya di da...we beat the E4. Afterwards, *fill in the blank* happens and we are able to battle the game's mascot(whichever version you pick). We go to the Battle Frontier....The end, haha.
What is the difference in the games you may ask? If you actually bothered to read, each team would play a much bigger role in the story you're following than the other depending on the version you have, with the other's actions going almost unnoticed by yourself(a la Ruby and Sapphire-ish). In the end, they are combined and Rayquaza saves the day with a 3D cutscene(Emerald-ish), except it leaves and damage has been already done to the tower, so it is unaccessible until after the E4. For whatever reason, you are also only able to catch your version's mascot.
Both teams(in the different versions) can still have the same ideas like the obvious Weather institute and stuff, but the differences in other schemes would be Magma working more with the Earth, while Aqua is more involved with Water type stuff.
How does that sound?