Pokémon Emerald beta
Very little was changed in Emerald, in relation to Ruby and Sapphire Versions, with the exception of the Battle Frontier and storyline tweaks to better include the legendaries Kyogre, Groudon, and Rayquaza. While there is no evidence to suggest the storyline was changed seriously, there is evidence that the Battle Frontier was changed slightly in various stages of development, however, these changes are minor and strictly relate almost entirely to building placements and static objects, such as fences.
Kanto and the Sevii Islands
While the areas are not at all accessible, the names of all Kanto and Sevii Islands locations, as well as Ruby and Sapphire locations, are in Emerald. This can be seen on a Pokémon's status screen, which will indicate the location a Pokémon was caught in Kanto. This may indicate that Kanto was initially to be included in the game, or that Emerald was built off the source code of FireRed and LeafGreen.
While Ruby and Sapphire, the base versions of Emerald, had upconverted Generation II music in their coding, Emerald contains the music from FireRed and LeafGreen in addition to its own themes.
A new, empty header included after the empty Kanto and Sevii Islands ones is named "Special Area". There is no actual information on what would have been included in this area.