In all honesty, I'm not overly concerned with the story of Emerald. Again, simply from what I've seen of it, it's similar to RS, but with two evil teams instead of one and somewhat changed ordering of routes and cities later on. That's assuming that there are RSE remakes, though. They could do sequels like with BW, or they could do a single Emerald remake, or they could just say "screw it" and save them for Gen VI, or just never do them at all. I'd imagine, though, that they'd use RS as a base for remakes, or recombine the story in such a way to reconcile both Rayquaza's interference and the two version's differences.
I don't see how Yellow is relevant to anything RGB. It's a separate game based off the anime that still follows mostly the same story progression.
The Gamestop in my area I know still carries GBA games, and they recently sent me an offer for buy2get1free pre-owned games. If I can't get it there, I could probably buy or trade an Emerald game off a friend of mine. That, or I could trade you my Sapphire cart for your Emerald cart over the Intergoogle.