Alpha and Omega seem more suited to Xerneas and Yveltal's themes (with beginning=creation and ending=destruction, respectively) in my opinion, but whatever... I can see how OmegaRuby could tie into the "From dust you came,
and to dust you shall return" phrase (based off of Genesis 3:19 from the Bible), although that particular phrase/comparison doesn't seem to leave room for water...
http://en.wikipedia.org/wiki/Ash_Wednesday#cite_note-4 Maybe
AlphaRuby (OMG, I keep typing AlphaRuby instead of AlphaSapphire!) is referring to the principle that
water is essential for all life/living things (with water commonly being perceived as
a restorative, nourishing, life-giving agent)...?
I think it might be following the pattern of X and Y in a way, considering that α and Ω are letters, except in the Greek alphabet.
Hmm; that could be plausible, too - other than "XY", the only letters I see paired up frequently enough are "AZ"/"α and Ω".. (/inb4theoriesrelatedtothecharacterAZofKalos)
I'm pretty convinced OR/AS will be a decade or so in the future from R/S/E in order to include mega evolutions without leaving a gaping plot hole. In that amount of time, anything could have changed in Hoenn, including new bad guy teams called Alpha and Omega. Though that would be a bit predictable, wouldn't it?
I don't think that the absence of Mega Evolutions would be that much of a plot hole, especially since they are triggered by Mega Stones, so one could just say that people didn't dig hard enough for whatever Mega Stones are lying around in Hoenn, if any.. XD (or that people in Kalos were more inclined to master Mega Evolution and news didn't spread around to Hoenn or something).. I just see Mega Evolutions as another "feature" (akin to Abilities), and I didn't see
Pokemon FireRed/
LeafGreen go out of its way too much to explain the existence/presence of Abilities and holdable items...
There could be a certain meaning behind it, but if I'm gonna be honest, I think they might just be spewing out ideas for titles at this point. I remember everyone was speculating about how X and Y might've been related to chromosomes in some way, or something about perspective with the x- and y-axis, but in the end, the titles had nothing to do with the games. There wasn't really any significance to the names of Heartgold and Soulsilver either. So I wouldn't get my hopes up about some specific meaning behind the names, at least not anything related to the actual storyline of the game.
It kind of does look like there aren't that many creative things to "oppose/act as counterparts" to each other that would make much sense for the
Pokemon franchise, although; "Alpha" and "Omega" for Kyogre and Groudon do seem a bit out of left field (and more fitting for Xerneas and Yveltal, in my opinion). Although there usually aren't direct meanings and you kind of have to stretch to extract meanings out of most of the core series
Pokemon game titles other than
Pokemon Gold/Silver and
Pokemon Black/White, XY tie in somewhat with
the Cartesian coordinate system and using (x, y, z) coordinates to interact in 3 dimensions (assuming that Zygarde ties into Xerneas and Yveltal somehow by representing depth or something).
As for
Pokemon HeartGold and SoulSilver, I can't find any immediate significance for the term "SoulSilver", but with "HeartGold", you could interpret it as the phrase "heart of gold" and meaning "pure-heartedness", tying into the
Pokemon Crystal and
Pokemon Y Pokedex entries that mention that Ho-Oh "will reveal itself before a pure-hearted Trainer by shining its bright, rainbow-colored wings"... But who knows, maybe the "Alpha" and "Omega" prefixes will have some significance revealed later on, possibly tying in with the Cave of Origin and Mt. Pyre..?