In wolf packs, I believe, "alphas" are the head of the pack. Omegas...may be the lower level guys, I'unno, I'm remembering this from an old TV ad. If this is correct, then it also sort of holds up for here - Kyogre can beat Groudon in a straight fight most of the time (has an ability that increases its STAB, which also hits Groudon for super effective damage). Of course, saying Alpha Sapphire would be better because of this is idiotic, considering they're both mostly the same game, as per Pokémon tradition.
Ah that's a fair point. In animals the dominant members are referred to as alphas, though I've never heard any term for the other members. so I guess it's just not a commonly used term. But in terms of the games canon Groudon and Kyogre are meant to be equals (yeah they're not, Kyogre's gonna win that fight every time cause super effective STAB on a physical attacker/defender, not special) so it'd make sense to interpret alpha and omega as beginning and end.