Probably because alpha and omega are words that have been horribly overused by kids shows aimed at boys and 12 year old and under boys as well.
Hell I was one of them when I was 11-12. (I think my oldest username was AlphaKid)
Fire, leaf, heart, soul aren't in the same realm as alpha and omega. They just sound stupid. Ruby and sapphire have pleeenty of names they could've done that sound better. Crimson ruby? things like that. Would've sounded a lot better.
Kind of a minor nitpick too but the omega and alpha title works with any of the titles just as well too. they're not really "fitting" because of that. Alpha red, omega green? Alpha gold, omega silver? fits just as well.
In the end it really, really doesn't matter and i'm bitching about virtually nothing, but meh. I'd rather they make real pokemon games rather than shitty nostalgia-tripping remakes that bring nothing to the table.