While I do think it is unlikely, I'm not going to rule out anything or say something is in 100% "for realz" simply due to I don't know. For the sake of discussion, I think incorporating story elements from Crystal in HG/SS was easier due to it being a plot to better flesh out Suicune, Entei and Raikou. While in Emerald it was a much more drastic change to Hoenn's entire plot, where Team Magma and Aqua bring both box legends to the surface. It doesn't seem to outlandish to think they might do it simply as a way to make more money, I'm sure there are many more other than just myself who would be willing to buy it if Gamefreak & co. DID end up deciding to actually do something at all like that.
Also, just to nit-pick, despite it's being inspired by the anime, I can't help but think that Yellow would be the "complimentary third title" to R&G/B considering blue is only a thing because green was "ugly."