As you notice in the box art for the games, Groudon and Kyogre's designs have either changed or these are their Mega evolutions / new formes. As you can see, Groudon's arms now have an "Omega" symbol (Ω) on them. As for Kyogre, it's "fins" or "wings" now have an Alpha symbol (A) on them.
This raises the question, what significance could Alpha and Omega have in the games? Will the storyline change from R / S? Have a connection to X / Y? Speculate below!
This raises the question, what significance could Alpha and Omega have in the games? Will the storyline change from R / S? Have a connection to X / Y? Speculate below!