In the original RSE, the meteor carrying Deoxys landed eons earlier than the one that threatens everyone in ORAS, creating Birth Island. Over time, the virus mutates into Deoxys, due to it's proximity near Pokemon.

In ORAS however, the meteor is blasted by the energy beam fired by King AZ. Due to the Ultimate Weapon being being powered by the souls of dead Pokemon (Or Infinte Energy if you will), the virus now mutates on the meteor, and by the time it reaches Earth it has become Deoxys.

This beam of energy also has the side effect of slowing the speed of the meteor, hence why it arrives so much later in ORAS than in RSE

Thoughts?

Also headcanon thread I guess