Following the confusion yesterday Satoru Iwata has confirmed that the games are full scale remakes.
"Following its reveal yesterday, there has been some question as to the actual content of Pokémon Omega Ruby & Alpha Sapphire, as to whether they're remakes or new versions due to the wording of the announcement. During the Investor Briefing today, Satoru Iwata confirmed that Pokémon Omega Ruby & Pokémon Alpha Sapphire are full-remakes of the 2002 releases, Pokémon Ruby & Sapphire. We'll bring more on these games as it comes"
Source:
http://www.serebii.net/index2.shtml