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In general Pokemon lore, Groudon and Kyogre basically created the world as it is now, Groudon forming the land and Kyogre forming the oceans. In the game Team Aqua and Team Magma want to cause the end of the world. This brings it full circle as Groudon and Kyogre brings "the beginning" while the influences of Team Aqua and Team Magma brings "the end".
Yeah, it’s possible that Alpha and Omega were just chosen because it would just make sense to follow the pattern that was started with the Kanto remakes.Well there wasn't much relation to Heart and Soul in HGSS so I don't think the words Alpha and Omega will play too much apart.
You can just barely make out the Omega symbol, but the Alpha symbol seems to be pretty obvious in the design (although it probably wasn’t though of at the time).Team Magma logo has visible Omega in it, the same goes for Aqua logo and Alpha.
The letter Alpha has a tie to the moon as well, and that has to do with the tides of the oceans.
These remake names had it coming since Ruby and Sapphire's release.
Groudon's hand- Omega marking. Kyorge's fin- Alpha Marking.
Aqua Logo - Stylized Alpha. Magma Logo - Stylized Omega.
...Does it really have a deeper meaning than this? No, I don't think so.
In religion (islam) and in science, life is said to have originated from water so that's Alpha for you. Human beings live on the ground and they are the species that will bring about the end of the world (lol) so thats omega for you.
Just my 2 cents :3