And it's not likely that its going to be the 3dd if it is in this gen so that may not work.
I've played thru all gen 3 games can someone tell me what makes emerald better story wise than ruby and sapphire ? To my knowledge its only that both teams are able to be fought, Rayquaza came and calmed down the beast( seriously guys your gonna call that a huge role in the game that if it doesn't have that one cutscene the games gonna be ruined) and gym leader and champion were the different
I say stick to the Ruby and Sapphire version differences. Give your rival and Wally a bigger role or create a new one all together . If you have ruby you would go after team magma and Wally and or the new character will go after aqua and vice versa. Therefore both teams are In each game with version differences , both pokemon get summoned so Rayquaza would still be part of the story
And as far as keys
Ruby key ( when unlocked in ruby offers a post game magma quest kind like sevii islands. But when transferred to sapphire it unlocks different magma quest and magma boss battle since in sapphire you didn't fight team magma. And special dungeon that gives you groudon with special attack and that is shiny ) and vice versa
See that was easy lol