Pokemon Omega Ruby and Alpha Sapphire are a "fresh take" on the original Game Boy Advance titles.
Update: Nintendo president Satoru Iwata clarified in a financial results briefing that Pokemon Omega Ruby and Alpha Sapphire are "full remakes," meaning the pair of games will not be a spin-off or a sequel to the original Ruby and Sapphire.
Nintendo announced today the 3DS titles Pokemon Omega Ruby and Alpha Sapphire, set to launch in November worldwide. They are remakes of the Game Boy Advance titles Pokemon Ruby and Pokemon Sapphire. While the new titles are remakes, Nintendo stated they are a "fresh take" on Ruby and Sapphire.
Ruby and Sapphire are set in the Hoenn region where two crime syndicates are trying to use Pokemon to change Hoenn's climate to either increase landmass or water levels. The starter Pokemon include Torchic, Mudkip, and Treecko, and the legendary Pokemon are Groudon and Kyogre. Ruby and Sapphire were the two games in the series to introduce double battles.
What Nintendo will add to Omega Ruby and Alpha Sapphire is unknown at this point, but the artwork of legendary Pokemon Groudon and Kyogre on the box art for the 3DS titles differs enough from the original artwork to make it look like they could be Mega Evolutions, a system Pokemon X and Y introduced.
Nintendo has remade past Pokemon games twice before: Blue and Red were remade to FireRed and LeafGreen and then Gold and Silver were remade to HeartGold and SoulSilver.
Source: Pokemon Company