Thematically, Omega can be used to represent the end, whereas Alpha can be used to represent the beginning. I don't know why Ruby was assigned Omega instead of Alpha, but when you look at it from a thematic perspective, it doesn't make that much of a difference. I'm sure we'll find out when the games are released.
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It's like diagonal billing, something they do when two big stars are in the same work. One is in the upper right, the other is lower left. If you read them top to bottom, one star is listed first, but if you read them left to right, the other comes first, so both egos are sated. It's the same deal here.
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