I believe GF will add Groudon/Kyogre encounter after Weather Crisis because Emerald's story doesn't have any obligatory battle with any legendary. Rayquaza is available but there is no any obligation to battle with it. That could mean GF planned Groudon/Kyogre encounter after Weather Crisis in R/S remakes already during Emerald's development.
You mean that Game Freak has been planning for nearly 10 years for a remake? Doubt it, big time. My brother has Emerald and I believe he captured his Rayquaza right after the Weather Crisis. If the battle isn't obligatory, it might just be a hole in the game left from remaking Ruby and Sapphire into Emerald.
R/S/E look like the last Pokemon games capable of having their stories fused with each other and having two remakes because their differences doesn't really rule out each other. It's totally different than D/P/Pt because Platinum's story seems to be impossible to be fused with Diamond or Pearl because there is obligatory battle with Giratina. That's why it seems very unlikely to have Diamond and Pearl remakes because it doesn't make any sense to ignore battle with Giratina and move to Dialga or Palkia.
I agree with you here, but this can also be applied to R/S/E as well, as D/P/Pt do the same basic thing that R/S/E do: Take the first 2 games and combine them for a unique 3rd version remake.
And I don't agree with saying that adding Kyogre/Groudon encounter after Emerald's Weather Crisis would make Emerald's story flawed and inaccurate. Rayquaza would do it's job to stop battle between Kyogre and Groudon, just like in Emerald. Rayquaza's legend would be fulfilled, just like in Emerald. Stopping one Kyogre or Groudon after Weather Crisis is not part of Rayquaza's legend, so I don't see any good reason against idea of mixing Emerald's story with Ruby or Sapphire, especially when there is actual possibility to make it happen in contrast to not being possible for Platinum to be mixed with Diamond or Pearl and probably for B2/W2 to be mixed with B/W.
My main issue against it is that it shifts the focus of the mascot Legendary (Groudon or Kyogre) onto Rayquaza, just like in Platinum when Giratina appears to stop Dialga and Palkia. Yes, GF could go do your idea, but it changes which Pokemon the story is focused. Rayquaza shouldn't be advertised as the most powerful Pokemon in a game that is focused around Groudon.
I think these remakes are the most anticipated actually and are certainly the ones on my list. You didn't hear much about Gold & Silver remakes, there was speculation but not as much as there is for Ruby & Sapphire which is kind of ironic considering they got a much lower reputation in comparison. This is good however as the more fans that demand it the more likely it's going to happen, not to mention the money which Nintendo love.
The only reason R/S/E remakes are anticipated are because some fans believe Game Freak is definitely going to make them, despite there being no evidence of it. The only real evidence supporters show are the previous remakes. Ever since HG/SS were announced, talks of possible R/S/E remakes have been going on. The assumption is that Game Freak has a tradition that they will not break.
The problem is though that there is no "tradition". The games were released like this:
1-Ruby and Sapphire
2-FireRed and LeafGreen [Remakes]
3-Emerald [3rd version]
4-Diamond and Pearl
5-Platinum [3rd version]
6-HeartGold and SoulSilver [Remakes]
7-Black and White
8-Black 2 and White 2 [Sequels]
These games were not released in an order than can be used to predict future releases. Though it is possible that R/S/E will come one day, I doubt it will be after B2/W2 just because "it's time for a remake!"