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Tiles change with time and weather, individual grass movement, music, Pokemon spawns, and individual region events, not to mention they'd have to start adding in a lot of new information to make up for the lack of story for each region and have to give everyone a valid reason to attend each region.
By the time you are through half of the third region, you also have a high chance of being level 100, which leaves the 4th and 5th region with nothing but level 100s which isn't very appealing to everyone.
You also have gamefreak's signature reason for making games to consider. We'd get 2 games missing a lot of Pokemon from one game to keep connectivity between the two games. Gamefreak will pull out a lot of pokemon to force players to trade between games and that could become an unappealing part of the game itself.
There is too much to think about when it comes to merging all the regions into one that in the end its too much work for little possible prize.
Home Consol, MMO, Mash up of the regions is an idea that all fans have had in the past, but its an idea with a lot of potential to kill the franchise only in the it gets harder to update department because if they release a new region they have to re-release the master game with all the new Pokemon, attacks, items, character, music, events (or even more new events).
Too much hassle, not enough positive feedback on it.
I definitely understand why they wouldn't want a home console release, and they probably wouldn't utilize all regions in one game, but it is possible to include 2-3 regions and still not have the opposing Pokemon be all at LV100 (which I also realize is a huge obstacle in creating these huge "mash-up" games). As for pulling out Pokemon for the "two-game" feature, people already find that either great or horrible, and I don't think their opinion would change too much, especially when having fun running from region to region.
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.