Why not, instead of releasing a remake of Ruby and Sapphire, just releasing a remake of Emerald. And then, same with FireRed and LeafGreen. Just release WaterBlue, or something. (Apologies for the lame name). So the release would be just them two. Just a suggestion.
Oh, and according to the Bulbapedia timeline, the Hoenn and Kanto stories occur at the same time. So, if GameFreak make the remakes so you can traverse to Kanto after beating the Elite Four in Hoenn, the final challenge would be Red, because he would be the current champion of Kanto.