Sorry, I didn't express myself very well.I'm not following this logic. If HGSS had Lugia and Ho-oh on the cover, allowed us to capture both and also included Crystals storyline then what makes you so sure that the same thing can't happen with these games?
In all three of those games (GSC) you could catch all the legends. Ruby and Sapphire were the first to feature version exclusive legends. HGSS featured the Suicune aspect of Crystal but in HG you got Ho-Oh first in SS you got Lugia just as in the originals. If ORAS follows Emerald's storyline, shouldn't the games be Emerald remakes not Ruby and Sapphire ones? One of the big things of Ruby and Sapphire was you could only catch Groudon or Kyogre. Despite Emerald having the better and more complete plot, I can't see you getting both legends in the same game.