One of the changes could be so Rayquaza probably only takes out one of them(the opposite) while you're left with handling the one standing(your mascot).
I think there's a huge misunderstanding about what happens at the end of the Weather Crisis. Rayquaza never actually battles Groudon and Kyogre. It has the ability/authority to calm the two of them, not by literally defeating them, but something about it's very presence calms Groudon and Kyogre. That's why it is regarded as the Trio Leader, it's like they have some kind of respect for Rayquaza for whatever reason.
Or, like you said, since we are getting B2 and W2, we could possibly see one Emerald remake as GF is being more unpredictable now, but I still see it unlikely. ;) See? Not gonna shoot off your idea entirely as I'm hoping for a 3rd gen remake period, haha.
I'm kinda torn between the 2. Personally, I'd much rather have a new Ruby since I have the original. But my brain tells me it might make more sense for just an Emerald remake, but that's only if they wanted to keep the Weather Crisis story in it. It's all really confusing.
Also, look for the Regis in B2/W2. If they're in those games, I'd say chances are that we won't be seeing R/S/E remakes. BUT, if they aren't there, chances are better.
True but you could get Ho-oh & Lugia in FRLG from Navel Rock and you saw what happened, just because legendaries exclusive to that game are available in other games doesn't rule out the need of a remake, there are other factors that comply.
Those were events, and if I'm not mistaken, you had to actually go somewhere to download the event, you couldn't just use it like Wi-Fi at your home. Ho-oh and Lugia were not easily obtainable in anyway before HG/SS because of these:
1=Navel Rock was an Event, and the old Events were much harder to get than today.
2=Ho-oh was also in Colosseum, but you had to finish the story mode AND Mt. Battle. You'd also have to own a Gamecube, link cable and other things necessary to trade to obtain the Ho-oh.
3=XD had Lugia, but again, you'd have to have a Gamecube and the other stuff if you wanted it on your GBA game.
So while they were in previous games, they weren't exactly easy to come by. The difference between Groudon and Kyogre from Lugia and Ho-oh is that in both HG/SS and in R/S/E, they were encountered normally and did not require anything extra to obtain them.