The "lack of story," though, is exactly the reason why I bring up that possibility. Having more regions will allow for more experiments with the story, which is honestly what the franchise needs right now.
And as for "rereleasing the master game" when an update happens, the 3DS is compatible with DLC. I'm not entirely sure how that would work, because as you've said they would be pushing it in terms of data space, but it's certainly not an impossible thing.
I really wouldn't be surprised if we saw a new game with Hoenn as an extra region, with that in itself serving as our remakes.
All remakes we've had so far are actually the third version remade but with the version differences of the first two games applied to them. For instance, the Eusine and Suicune sub-plot in HGSS.
As to how that will work with RS remakes, I don't know, but it's almost certain we will see some elements of Emerald in there as well.
DS games were compatible with DLC. Pokemon B/W and B2W2 Has Downloadable content. If you mean data added to the game that didn't exist in the original game like say Hearthfire or Dawnguard for Skyrim, I don't think they are that compatible as force feeding new data into a chip like that corrodes the data unlike a disc where the save files are stored separately and the DLC doesn't effect the original game data at all. I haven't seen any DS or 3DS games with full DLC that wasn't already programmed into the games in some way shape or form and just needed the DLC to unlock items or creatures to fully activate them, like all of the Pokemon Downloads from B/W/D/P/Pt/HG/SS.
As for thirds always appearing in the remakes, that isn't completely true. Even though Yellow was a Fourth title in Japan it is acknowledged to be the Third Title to Pokemon everywhere else and none of the extra changes from Yellow were added into FR/LG.
While I do support that Emerald's Magma Hideout and Rayquaza being able to stop the fight should be added, we don't have definitive proof that they will be there. Gamefreak can always just ignore the events of Emerald since they are already identical to the events in Ruby and Sapphire.