Yeah, I don't think they will be called Magma Ruby and Aqua Sapphire seeing as Groundon isn't a Magma Pokemon, but then again, what do Ho-Oh and Lugia have to do with Heart and Soul respectively.
I was thinking along the lines of Dry Ruby and Wet Sapphire though the latter doesn't sound so hot. So Solid Ruby and Liquid Sapphire, in terms of state of matter (Rayquaza being gas as in air). But they could make a trio based on that in future games.
Also, I don't want them to replace May and Brendan so what we the story be? A carbon-copy? No one would want that. So I was thinking that they failed the Hoenn League, traveled to other regions, failed, then come back to start all over again. So it can appeal to a new audience. They are older. Regarding Gym Leaders, maybe they'll all say "Oh I recognise you, this Gym has changed a lot since you last came, it won't be easy" etc. And Wally is League Champion after so long. Brendan/May will be more rivalry, the other person stayed in Hoenn, stopped training to help Prof. Birch more, but upon seeing the other person, wants to start over again. Steven is there too. No Isshu Pokemon will be in the wild, but maybe be imported to the Safari zone. The team will be Sky Team, after Rayquaza? Or Magma and Aqua come back...
That's all :)
I miss Hoenn :(